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_tsinfermodule.c
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_tsinfermodule.c
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#define PY_SSIZE_T_CLEAN
#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
#include <Python.h>
#include <numpy/arrayobject.h>
#include <structmember.h>
#include <float.h>
#include <stdbool.h>
#include "lib/tsinfer.h"
#if PY_MAJOR_VERSION >= 3
#define IS_PY3K
#endif
#define MODULE_DOC \
"Low-level tsinfer interface."
static PyObject *TsinfLibraryError;
typedef struct {
PyObject_HEAD
ancestor_builder_t *builder;
} AncestorBuilder;
typedef struct {
PyObject_HEAD
tree_sequence_builder_t *tree_sequence_builder;
} TreeSequenceBuilder;
typedef struct {
PyObject_HEAD
ancestor_matcher_t *ancestor_matcher;
TreeSequenceBuilder *tree_sequence_builder;
} AncestorMatcher;
static void
handle_library_error(int err)
{
if (err == TSI_ERR_NO_MEMORY) {
PyErr_NoMemory();
} else {
PyErr_Format(TsinfLibraryError, "Error occured: %d", err);
}
}
static int
uint32_PyArray_converter(PyObject *in, PyObject **out)
{
PyObject *ret = PyArray_FROMANY(in, NPY_UINT32, 1, 1, NPY_ARRAY_IN_ARRAY);
if (ret == NULL) {
return NPY_FAIL;
}
*out = ret;
return NPY_SUCCEED;
}
/*===================================================================
* AncestorBuilder
*===================================================================
*/
static int
AncestorBuilder_check_state(AncestorBuilder *self)
{
int ret = 0;
if (self->builder == NULL) {
PyErr_SetString(PyExc_SystemError, "AncestorBuilder not initialised");
ret = -1;
}
return ret;
}
static void
AncestorBuilder_dealloc(AncestorBuilder* self)
{
if (self->builder != NULL) {
ancestor_builder_free(self->builder);
PyMem_Free(self->builder);
self->builder = NULL;
}
Py_TYPE(self)->tp_free((PyObject*)self);
}
static int
AncestorBuilder_init(AncestorBuilder *self, PyObject *args, PyObject *kwds)
{
int ret = -1;
int err;
static char *kwlist[] = {"num_samples", "num_sites", NULL};
int num_samples, num_sites;
int flags = 0;
self->builder = NULL;
if (!PyArg_ParseTupleAndKeywords(args, kwds, "ii", kwlist,
&num_samples, &num_sites)) {
goto out;
}
self->builder = PyMem_Malloc(sizeof(ancestor_builder_t));
if (self->builder == NULL) {
PyErr_NoMemory();
goto out;
}
Py_BEGIN_ALLOW_THREADS
err = ancestor_builder_alloc(self->builder, num_samples, num_sites, flags);
Py_END_ALLOW_THREADS
if (err != 0) {
handle_library_error(err);
goto out;
}
ret = 0;
out:
return ret;
}
static PyObject *
AncestorBuilder_add_site(AncestorBuilder *self, PyObject *args, PyObject *kwds)
{
int err;
static char *kwlist[] = {"site_id", "time", "genotypes", NULL};
PyObject *ret = NULL;
int site_id;
double time;
PyObject *genotypes = NULL;
PyArrayObject *genotypes_array = NULL;
npy_intp *shape;
if (AncestorBuilder_check_state(self) != 0) {
goto out;
}
if (!PyArg_ParseTupleAndKeywords(args, kwds, "idO!", kwlist,
&site_id, &time, &PyArray_Type, &genotypes)) {
goto out;
}
genotypes_array = (PyArrayObject *) PyArray_FROM_OTF(genotypes, NPY_INT8,
NPY_ARRAY_IN_ARRAY);
if (genotypes_array == NULL) {
goto out;
}
if (PyArray_NDIM(genotypes_array) != 1) {
PyErr_SetString(PyExc_ValueError, "Dim != 1");
goto out;
}
shape = PyArray_DIMS(genotypes_array);
if (shape[0] != self->builder->num_samples) {
PyErr_SetString(PyExc_ValueError, "genotypes array wrong size.");
goto out;
}
Py_BEGIN_ALLOW_THREADS
err = ancestor_builder_add_site(self->builder, (tsk_id_t) site_id, time,
(allele_t *) PyArray_DATA(genotypes_array));
Py_END_ALLOW_THREADS
if (err != 0) {
handle_library_error(err);
goto out;
}
ret = Py_BuildValue("");
out:
Py_XDECREF(genotypes_array);
return ret;
}
static PyObject *
AncestorBuilder_make_ancestor(AncestorBuilder *self, PyObject *args, PyObject *kwds)
{
int err;
static char *kwlist[] = {"focal_sites", "ancestor", NULL};
PyObject *ancestor = NULL;
PyArrayObject *ancestor_array = NULL;
PyObject *focal_sites = NULL;
PyArrayObject *focal_sites_array = NULL;
size_t num_focal_sites;
size_t num_sites;
tsk_id_t start, end;
npy_intp *shape;
if (AncestorBuilder_check_state(self) != 0) {
goto fail;
}
if (!PyArg_ParseTupleAndKeywords(args, kwds, "OO!", kwlist,
&focal_sites, &PyArray_Type, &ancestor)) {
goto fail;
}
num_sites = self->builder->num_sites;
focal_sites_array = (PyArrayObject *) PyArray_FROM_OTF(focal_sites, NPY_INT32,
NPY_ARRAY_IN_ARRAY);
if (focal_sites_array == NULL) {
goto fail;
}
if (PyArray_NDIM(focal_sites_array) != 1) {
PyErr_SetString(PyExc_ValueError, "Dim != 1");
goto fail;
}
shape = PyArray_DIMS(focal_sites_array);
num_focal_sites = shape[0];
if (num_focal_sites == 0 || num_focal_sites > num_sites) {
PyErr_SetString(PyExc_ValueError, "num_focal_sites must > 0 and <= num_sites");
goto fail;
}
ancestor_array = (PyArrayObject *) PyArray_FROM_OTF(ancestor, NPY_INT8,
NPY_ARRAY_INOUT_ARRAY);
if (ancestor_array == NULL) {
goto fail;
}
if (PyArray_NDIM(ancestor_array) != 1) {
PyErr_SetString(PyExc_ValueError, "Dim != 1");
goto fail;
}
shape = PyArray_DIMS(ancestor_array);
if (shape[0] != num_sites) {
PyErr_SetString(PyExc_ValueError, "input ancestor wrong size");
goto fail;
}
Py_BEGIN_ALLOW_THREADS
err = ancestor_builder_make_ancestor(self->builder, num_focal_sites,
(int32_t *) PyArray_DATA(focal_sites_array),
&start, &end, (int8_t *) PyArray_DATA(ancestor_array));
Py_END_ALLOW_THREADS
if (err != 0) {
handle_library_error(err);
goto fail;
}
Py_DECREF(focal_sites_array);
Py_DECREF(ancestor_array);
return Py_BuildValue("ii", start, end);
fail:
Py_XDECREF(focal_sites_array);
PyArray_XDECREF_ERR(ancestor_array);
return NULL;
}
static PyObject *
AncestorBuilder_ancestor_descriptors(AncestorBuilder *self)
{
PyObject *ret = NULL;
PyObject *descriptors = NULL;
PyObject *py_descriptor = NULL;
PyArrayObject *site_array = NULL;
ancestor_descriptor_t *descriptor;
size_t j;
npy_intp dims;
int err;
if (AncestorBuilder_check_state(self) != 0) {
goto out;
}
err = ancestor_builder_finalise(self->builder);
if (err != 0) {
handle_library_error(err);
goto out;
}
/* ancestor_builder_print_state(self->builder, stdout); */
descriptors = PyTuple_New(self->builder->num_ancestors);
if (descriptors == NULL) {
goto out;
}
for (j = 0; j < self->builder->num_ancestors; j++) {
descriptor = &self->builder->descriptors[j];
dims = descriptor->num_focal_sites;
site_array = (PyArrayObject *) PyArray_SimpleNew(1, &dims, NPY_INT32);
if (site_array == NULL) {
goto out;
}
memcpy(PyArray_DATA(site_array), descriptor->focal_sites,
descriptor->num_focal_sites * sizeof(tsk_id_t));
py_descriptor = Py_BuildValue("dO", descriptor->time, site_array);
if (py_descriptor == NULL) {
Py_DECREF(site_array);
goto out;
}
PyTuple_SET_ITEM(descriptors, j, py_descriptor);
}
/* j = 0; */
/* /1* It's not great that we're breaking encapsulation here and looking */
/* * directly in to the builder's data structures. However, it's quite an */
/* * awkward set of data to communicate, so it seems OK. *1/ */
/* for (f = self->builder->num_samples; f > 0; f--) { */
/* for (a = self->builder->frequency_map[f].head; a != NULL; a = a->next) { */
/* map_elem = (pattern_map_t *) a->item; */
/* dims = map_elem->num_sites; */
/* site_array = (PyArrayObject *) PyArray_SimpleNew(1, &dims, NPY_INT32); */
/* if (site_array == NULL) { */
/* goto out; */
/* } */
/* site_array_data = (int32_t *) PyArray_DATA(site_array); */
/* /1* The elements are listed backwards, so reverse them *1/ */
/* k = map_elem->num_sites - 1; */
/* for (s = map_elem->sites; s != NULL; s = s->next) { */
/* site_array_data[k] = (int32_t) s->site; */
/* k--; */
/* } */
/* descriptor = Py_BuildValue("kO", (unsigned long) f, site_array); */
/* if (descriptor == NULL) { */
/* Py_DECREF(site_array); */
/* goto out; */
/* } */
/* PyTuple_SET_ITEM(descriptors, j, descriptor); */
/* j++; */
/* } */
/* } */
ret = descriptors;
descriptors = NULL;
out:
Py_XDECREF(descriptors);
return ret;
}
static PyObject *
AncestorBuilder_get_num_sites(AncestorBuilder *self, void *closure)
{
PyObject *ret = NULL;
if (AncestorBuilder_check_state(self) != 0) {
goto out;
}
ret = Py_BuildValue("k", (unsigned long) self->builder->num_sites);
out:
return ret;
}
static PyObject *
AncestorBuilder_get_num_ancestors(AncestorBuilder *self, void *closure)
{
PyObject *ret = NULL;
if (AncestorBuilder_check_state(self) != 0) {
goto out;
}
ret = Py_BuildValue("k", (unsigned long) self->builder->num_ancestors);
out:
return ret;
}
static PyMemberDef AncestorBuilder_members[] = {
{NULL} /* Sentinel */
};
static PyGetSetDef AncestorBuilder_getsetters[] = {
{"num_sites", (getter) AncestorBuilder_get_num_sites, NULL, "The number of sites."},
{"num_ancestors", (getter) AncestorBuilder_get_num_ancestors, NULL, "The number of ancestors."},
{NULL} /* Sentinel */
};
static PyMethodDef AncestorBuilder_methods[] = {
{"add_site", (PyCFunction) AncestorBuilder_add_site,
METH_VARARGS|METH_KEYWORDS,
"Adds the specified site to this ancestor builder."},
{"make_ancestor", (PyCFunction) AncestorBuilder_make_ancestor,
METH_VARARGS|METH_KEYWORDS,
"Makes the specified ancestor."},
{"ancestor_descriptors", (PyCFunction) AncestorBuilder_ancestor_descriptors,
METH_NOARGS,
"Returns a list of ancestor (frequency, focal_sites) tuples."},
{NULL} /* Sentinel */
};
static PyTypeObject AncestorBuilderType = {
PyVarObject_HEAD_INIT(NULL, 0)
"_tsinfer.AncestorBuilder", /* tp_name */
sizeof(AncestorBuilder), /* tp_basicsize */
0, /* tp_itemsize */
(destructor)AncestorBuilder_dealloc, /* tp_dealloc */
0, /* tp_print */
0, /* tp_getattr */
0, /* tp_setattr */
0, /* tp_reserved */
0, /* tp_repr */
0, /* tp_as_number */
0, /* tp_as_sequence */
0, /* tp_as_mapping */
0, /* tp_hash */
0, /* tp_call */
0, /* tp_str */
0, /* tp_getattro */
0, /* tp_setattro */
0, /* tp_as_buffer */
Py_TPFLAGS_DEFAULT, /* tp_flags */
"AncestorBuilder objects", /* tp_doc */
0, /* tp_traverse */
0, /* tp_clear */
0, /* tp_richcompare */
0, /* tp_weaklistoffset */
0, /* tp_iter */
0, /* tp_iternext */
AncestorBuilder_methods, /* tp_methods */
AncestorBuilder_members, /* tp_members */
AncestorBuilder_getsetters, /* tp_getset */
0, /* tp_base */
0, /* tp_dict */
0, /* tp_descr_get */
0, /* tp_descr_set */
0, /* tp_dictoffset */
(initproc)AncestorBuilder_init, /* tp_init */
};
/*===================================================================
* TreeSequenceBuilder
*===================================================================
*/
static int
TreeSequenceBuilder_check_state(TreeSequenceBuilder *self)
{
int ret = 0;
if (self->tree_sequence_builder == NULL) {
PyErr_SetString(PyExc_SystemError, "TreeSequenceBuilder not initialised");
ret = -1;
}
return ret;
}
static void
TreeSequenceBuilder_dealloc(TreeSequenceBuilder* self)
{
if (self->tree_sequence_builder != NULL) {
tree_sequence_builder_free(self->tree_sequence_builder);
PyMem_Free(self->tree_sequence_builder);
self->tree_sequence_builder = NULL;
}
Py_TYPE(self)->tp_free((PyObject*)self);
}
static int
TreeSequenceBuilder_init(TreeSequenceBuilder *self, PyObject *args, PyObject *kwds)
{
int ret = -1;
int err;
static char *kwlist[] = {"num_alleles", "max_nodes", "max_edges", NULL};
PyArrayObject *num_alleles = NULL;
unsigned long max_nodes = 1024;
unsigned long max_edges = 1024;
unsigned long num_sites;
npy_intp *shape;
int flags = 0;
self->tree_sequence_builder = NULL;
if (!PyArg_ParseTupleAndKeywords(args, kwds, "O&|kk", kwlist,
uint32_PyArray_converter, &num_alleles,
&max_nodes, &max_edges)) {
goto out;
}
shape = PyArray_DIMS(num_alleles);
num_sites = shape[0];
self->tree_sequence_builder = PyMem_Malloc(sizeof(tree_sequence_builder_t));
if (self->tree_sequence_builder == NULL) {
PyErr_NoMemory();
goto out;
}
err = tree_sequence_builder_alloc(self->tree_sequence_builder,
num_sites, PyArray_DATA(num_alleles),
max_nodes, max_edges, flags);
if (err != 0) {
handle_library_error(err);
goto out;
}
ret = 0;
out:
Py_XDECREF(num_alleles);
return ret;
}
static PyObject *
TreeSequenceBuilder_add_node(TreeSequenceBuilder *self, PyObject *args, PyObject *kwds)
{
int err;
PyObject *ret = NULL;
static char *kwlist[] = {"time", "flags", NULL};
double time;
int flags = 1;
if (TreeSequenceBuilder_check_state(self) != 0) {
goto out;
}
if (!PyArg_ParseTupleAndKeywords(args, kwds, "d|i", kwlist, &time,
&flags)) {
goto out;
}
err = tree_sequence_builder_add_node(self->tree_sequence_builder,
time, (uint32_t) flags);
if (err < 0) {
handle_library_error(err);
goto out;
}
ret = Py_BuildValue("i", err);
out:
return ret;
}
static PyObject *
TreeSequenceBuilder_add_path(TreeSequenceBuilder *self, PyObject *args, PyObject *kwds)
{
int err;
PyObject *ret = NULL;
int flags = 0;
PyObject *left = NULL;
PyArrayObject *left_array = NULL;
PyObject *right = NULL;
PyArrayObject *right_array = NULL;
PyObject *parent = NULL;
PyArrayObject *parent_array = NULL;
int child;
size_t num_edges;
npy_intp *shape;
int compress = 1;
int extended_checks = 0;
static char *kwlist[] = {"child", "left", "right", "parent",
"compress", "extended_checks", NULL};
if (TreeSequenceBuilder_check_state(self) != 0) {
goto out;
}
if (!PyArg_ParseTupleAndKeywords(args, kwds, "kOOO|ii", kwlist,
&child, &left, &right, &parent, &compress, &extended_checks)) {
goto out;
}
if (compress) {
flags = TSI_COMPRESS_PATH;
}
if (extended_checks) {
flags |= TSI_EXTENDED_CHECKS;
}
/* left */
left_array = (PyArrayObject *) PyArray_FROM_OTF(left, NPY_UINT32, NPY_ARRAY_IN_ARRAY);
if (left_array == NULL) {
goto out;
}
if (PyArray_NDIM(left_array) != 1) {
PyErr_SetString(PyExc_ValueError, "Dim != 1");
goto out;
}
shape = PyArray_DIMS(left_array);
num_edges = shape[0];
/* right */
right_array = (PyArrayObject *) PyArray_FROM_OTF(right, NPY_UINT32, NPY_ARRAY_IN_ARRAY);
if (right_array == NULL) {
goto out;
}
if (PyArray_NDIM(right_array) != 1) {
PyErr_SetString(PyExc_ValueError, "Dim != 1");
goto out;
}
shape = PyArray_DIMS(right_array);
if (shape[0] != num_edges) {
PyErr_SetString(PyExc_ValueError, "right wrong size");
goto out;
}
/* parent */
parent_array = (PyArrayObject *) PyArray_FROM_OTF(parent, NPY_INT32, NPY_ARRAY_IN_ARRAY);
if (parent_array == NULL) {
goto out;
}
if (PyArray_NDIM(parent_array) != 1) {
PyErr_SetString(PyExc_ValueError, "Dim != 1");
goto out;
}
shape = PyArray_DIMS(parent_array);
if (shape[0] != num_edges) {
PyErr_SetString(PyExc_ValueError, "parent wrong size");
goto out;
}
/* WARNING!! This isn't fully safe as we're using pointers to data that can
* be modified in Python. Must make sure that these arrays are not modified
* by other threads. */
Py_BEGIN_ALLOW_THREADS
err = tree_sequence_builder_add_path(self->tree_sequence_builder,
child, num_edges,
(tsk_id_t *) PyArray_DATA(left_array),
(tsk_id_t *) PyArray_DATA(right_array),
(tsk_id_t *) PyArray_DATA(parent_array),
flags);
Py_END_ALLOW_THREADS
if (err < 0) {
handle_library_error(err);
goto out;
}
ret = Py_BuildValue("");
out:
Py_XDECREF(left_array);
Py_XDECREF(right_array);
Py_XDECREF(parent_array);
return ret;
}
static PyObject *
TreeSequenceBuilder_add_mutations(TreeSequenceBuilder *self, PyObject *args, PyObject *kwds)
{
int err;
PyObject *ret = NULL;
PyObject *site = NULL;
PyArrayObject *site_array = NULL;
PyObject *derived_state = NULL;
PyArrayObject *derived_state_array = NULL;
int node;
size_t num_mutations;
npy_intp *shape;
static char *kwlist[] = {"node", "site", "derived_state", NULL};
if (TreeSequenceBuilder_check_state(self) != 0) {
goto out;
}
if (!PyArg_ParseTupleAndKeywords(args, kwds, "kOO", kwlist,
&node, &site, &derived_state)) {
goto out;
}
/* site */
site_array = (PyArrayObject *) PyArray_FROM_OTF(site, NPY_INT32, NPY_ARRAY_IN_ARRAY);
if (site_array == NULL) {
goto out;
}
if (PyArray_NDIM(site_array) != 1) {
PyErr_SetString(PyExc_ValueError, "Dim != 1");
goto out;
}
shape = PyArray_DIMS(site_array);
num_mutations = shape[0];
/* derived_state */
derived_state_array = (PyArrayObject *) PyArray_FROM_OTF(derived_state, NPY_INT8,
NPY_ARRAY_IN_ARRAY);
if (derived_state_array == NULL) {
goto out;
}
if (PyArray_NDIM(derived_state_array) != 1) {
PyErr_SetString(PyExc_ValueError, "Dim != 1");
goto out;
}
shape = PyArray_DIMS(derived_state_array);
if (shape[0] != num_mutations) {
PyErr_SetString(PyExc_ValueError, "derived_state wrong size");
goto out;
}
/* WARNING!! This isn't fully safe as we're using pointers to data that can
* be modified in Python. Must make sure that these arrays are not modified
* by other threads. */
Py_BEGIN_ALLOW_THREADS
err = tree_sequence_builder_add_mutations(self->tree_sequence_builder,
node, num_mutations,
(tsk_id_t *) PyArray_DATA(site_array),
(allele_t *) PyArray_DATA(derived_state_array));
Py_END_ALLOW_THREADS
if (err < 0) {
handle_library_error(err);
goto out;
}
ret = Py_BuildValue("");
out:
Py_XDECREF(site_array);
Py_XDECREF(derived_state_array);
return ret;
}
static PyObject *
TreeSequenceBuilder_restore_nodes(TreeSequenceBuilder *self, PyObject *args, PyObject *kwds)
{
int err;
PyObject *ret = NULL;
static char *kwlist[] = {"time", "flags", NULL};
PyObject *time = NULL;
PyArrayObject *time_array = NULL;
PyObject *flags = NULL;
PyArrayObject *flags_array = NULL;
npy_intp *shape;
size_t num_nodes;
if (TreeSequenceBuilder_check_state(self) != 0) {
goto out;
}
if (!PyArg_ParseTupleAndKeywords(args, kwds, "OO", kwlist, &time, &flags)) {
goto out;
}
/* time */
time_array = (PyArrayObject *) PyArray_FROM_OTF(time, NPY_FLOAT64, NPY_ARRAY_IN_ARRAY);
if (time_array == NULL) {
goto out;
}
if (PyArray_NDIM(time_array) != 1) {
PyErr_SetString(PyExc_ValueError, "Dim != 1");
goto out;
}
shape = PyArray_DIMS(time_array);
num_nodes = shape[0];
/* flags */
flags_array = (PyArrayObject *) PyArray_FROM_OTF(flags, NPY_UINT32, NPY_ARRAY_IN_ARRAY);
if (flags_array == NULL) {
goto out;
}
if (PyArray_NDIM(flags_array) != 1) {
PyErr_SetString(PyExc_ValueError, "Dim != 1");
goto out;
}
shape = PyArray_DIMS(flags_array);
if (shape[0] != num_nodes) {
PyErr_SetString(PyExc_ValueError, "flags array incorrect size");
goto out;
}
Py_BEGIN_ALLOW_THREADS
err = tree_sequence_builder_restore_nodes(self->tree_sequence_builder,
num_nodes,
(uint32_t *) PyArray_DATA(flags_array),
(double *) PyArray_DATA(time_array));
Py_END_ALLOW_THREADS
if (err != 0) {
handle_library_error(err);
goto out;
}
ret = Py_BuildValue("");
out:
Py_XDECREF(time_array);
Py_XDECREF(flags_array);
return ret;
}
static PyObject *
TreeSequenceBuilder_restore_edges(TreeSequenceBuilder *self, PyObject *args, PyObject *kwds)
{
int err;
PyObject *ret = NULL;
static char *kwlist[] = {"left", "right", "parent", "child", NULL};
size_t num_edges;
PyObject *left = NULL;
PyArrayObject *left_array = NULL;
PyObject *right = NULL;
PyArrayObject *right_array = NULL;
PyObject *parent = NULL;
PyArrayObject *parent_array = NULL;
PyObject *child = NULL;
PyArrayObject *child_array = NULL;
npy_intp *shape;
if (TreeSequenceBuilder_check_state(self) != 0) {
goto out;
}
if (!PyArg_ParseTupleAndKeywords(args, kwds, "OOOO", kwlist,
&left, &right, &parent, &child)) {
goto out;
}
/* left */
left_array = (PyArrayObject *) PyArray_FROM_OTF(left, NPY_INT32, NPY_ARRAY_IN_ARRAY);
if (left_array == NULL) {
goto out;
}
if (PyArray_NDIM(left_array) != 1) {
PyErr_SetString(PyExc_ValueError, "Dim != 1");
goto out;
}
shape = PyArray_DIMS(left_array);
num_edges = shape[0];
/* right */
right_array = (PyArrayObject *) PyArray_FROM_OTF(right, NPY_INT32, NPY_ARRAY_IN_ARRAY);
if (right_array == NULL) {
goto out;
}
if (PyArray_NDIM(right_array) != 1) {
PyErr_SetString(PyExc_ValueError, "Dim != 1");
goto out;
}
shape = PyArray_DIMS(right_array);
if (shape[0] != num_edges) {
PyErr_SetString(PyExc_ValueError, "right wrong size");
goto out;
}
/* parent */
parent_array = (PyArrayObject *) PyArray_FROM_OTF(parent, NPY_INT32, NPY_ARRAY_IN_ARRAY);
if (parent_array == NULL) {
goto out;
}
if (PyArray_NDIM(parent_array) != 1) {
PyErr_SetString(PyExc_ValueError, "Dim != 1");
goto out;
}
shape = PyArray_DIMS(parent_array);
if (shape[0] != num_edges) {
PyErr_SetString(PyExc_ValueError, "parent wrong size");
goto out;
}
/* child */
child_array = (PyArrayObject *) PyArray_FROM_OTF(child, NPY_INT32, NPY_ARRAY_IN_ARRAY);
if (child_array == NULL) {
goto out;
}
if (PyArray_NDIM(child_array) != 1) {
PyErr_SetString(PyExc_ValueError, "Dim != 1");
goto out;
}
shape = PyArray_DIMS(child_array);
if (shape[0] != num_edges) {
PyErr_SetString(PyExc_ValueError, "child wrong size");
goto out;
}
Py_BEGIN_ALLOW_THREADS
err = tree_sequence_builder_restore_edges(self->tree_sequence_builder,
num_edges,
(tsk_id_t *) PyArray_DATA(left_array),
(tsk_id_t *) PyArray_DATA(right_array),
(tsk_id_t *) PyArray_DATA(parent_array),
(tsk_id_t *) PyArray_DATA(child_array));
Py_END_ALLOW_THREADS
if (err != 0) {
handle_library_error(err);
goto out;
}
ret = Py_BuildValue("");
out:
Py_XDECREF(left_array);
Py_XDECREF(right_array);
Py_XDECREF(parent_array);
Py_XDECREF(child_array);
return ret;
}
static PyObject *
TreeSequenceBuilder_restore_mutations(TreeSequenceBuilder *self, PyObject *args, PyObject *kwds)
{
int err;
PyObject *ret = NULL;
static char *kwlist[] = {"site", "node", "derived_state", "parent", NULL};
size_t num_mutations;
PyObject *site = NULL;
PyArrayObject *site_array = NULL;
PyObject *node = NULL;
PyArrayObject *node_array = NULL;
PyObject *derived_state = NULL;
PyArrayObject *derived_state_array = NULL;
PyObject *parent = NULL;
PyArrayObject *parent_array = NULL;
npy_intp *shape;
if (TreeSequenceBuilder_check_state(self) != 0) {
goto out;
}
if (!PyArg_ParseTupleAndKeywords(args, kwds, "OOOO", kwlist,
&site, &node, &derived_state, &parent)) {
goto out;
}
/* site */
site_array = (PyArrayObject *) PyArray_FROM_OTF(site, NPY_INT32, NPY_ARRAY_IN_ARRAY);
if (site_array == NULL) {
goto out;
}
if (PyArray_NDIM(site_array) != 1) {
PyErr_SetString(PyExc_ValueError, "Dim != 1");
goto out;
}
shape = PyArray_DIMS(site_array);
num_mutations = shape[0];
/* node */
node_array = (PyArrayObject *) PyArray_FROM_OTF(node, NPY_INT32, NPY_ARRAY_IN_ARRAY);
if (node_array == NULL) {
goto out;
}
if (PyArray_NDIM(node_array) != 1) {
PyErr_SetString(PyExc_ValueError, "Dim != 1");
goto out;
}
shape = PyArray_DIMS(node_array);
if (shape[0] != num_mutations) {
PyErr_SetString(PyExc_ValueError, "node wrong size");
goto out;
}
/* derived_state */
derived_state_array = (PyArrayObject *) PyArray_FROM_OTF(derived_state, NPY_INT8,
NPY_ARRAY_IN_ARRAY);
if (derived_state_array == NULL) {
goto out;
}
if (PyArray_NDIM(derived_state_array) != 1) {
PyErr_SetString(PyExc_ValueError, "Dim != 1");
goto out;
}
shape = PyArray_DIMS(derived_state_array);
if (shape[0] != num_mutations) {
PyErr_SetString(PyExc_ValueError, "derived_state wrong size");
goto out;
}
/* parent */
parent_array = (PyArrayObject *) PyArray_FROM_OTF(parent, NPY_INT32, NPY_ARRAY_IN_ARRAY);
if (parent_array == NULL) {
goto out;
}
if (PyArray_NDIM(parent_array) != 1) {
PyErr_SetString(PyExc_ValueError, "Dim != 1");
goto out;
}
shape = PyArray_DIMS(parent_array);
if (shape[0] != num_mutations) {
PyErr_SetString(PyExc_ValueError, "parent wrong size");
goto out;
}
Py_BEGIN_ALLOW_THREADS
err = tree_sequence_builder_restore_mutations(self->tree_sequence_builder,
num_mutations,
(tsk_id_t *) PyArray_DATA(site_array),
(tsk_id_t *) PyArray_DATA(node_array),
(allele_t *) PyArray_DATA(derived_state_array));
/* NOTE: we are ignoring parent here! */
Py_END_ALLOW_THREADS
if (err != 0) {
handle_library_error(err);
goto out;
}
ret = Py_BuildValue("");
out:
Py_XDECREF(site_array);
Py_XDECREF(node_array);
Py_XDECREF(derived_state_array);
Py_XDECREF(parent_array);
return ret;
}
static PyObject *
TreeSequenceBuilder_dump_nodes(TreeSequenceBuilder *self)
{
int err;
PyObject *ret = NULL;
PyArrayObject *time = NULL;
PyArrayObject *flags= NULL;
npy_intp shape;
if (TreeSequenceBuilder_check_state(self) != 0) {
goto out;
}
shape = self->tree_sequence_builder->num_nodes;
time = (PyArrayObject *) PyArray_SimpleNew(1, &shape, NPY_FLOAT64);
flags = (PyArrayObject *) PyArray_SimpleNew(1, &shape, NPY_UINT32);
if (time == NULL || flags == NULL) {
goto out;
}
Py_BEGIN_ALLOW_THREADS
err = tree_sequence_builder_dump_nodes(self->tree_sequence_builder,
(uint32_t *) PyArray_DATA(flags),
(double *) PyArray_DATA(time));
Py_END_ALLOW_THREADS
if (err != 0) {
handle_library_error(err);
goto out;
}
ret = Py_BuildValue("OO", flags, time);
if (ret == NULL) {
goto out;
}
time = NULL;
flags = NULL;
out:
Py_XDECREF(time);
Py_XDECREF(flags);
return ret;
}
static PyObject *
TreeSequenceBuilder_dump_edges(TreeSequenceBuilder *self)
{
int err;
PyObject *ret = NULL;
PyArrayObject *left = NULL;
PyArrayObject *right = NULL;
PyArrayObject *parent = NULL;
PyArrayObject *child = NULL;
npy_intp shape;
if (TreeSequenceBuilder_check_state(self) != 0) {
goto out;
}
shape = tree_sequence_builder_get_num_edges(self->tree_sequence_builder);
left = (PyArrayObject *) PyArray_SimpleNew(1, &shape, NPY_INT32);
right = (PyArrayObject *) PyArray_SimpleNew(1, &shape, NPY_INT32);
parent = (PyArrayObject *) PyArray_SimpleNew(1, &shape, NPY_INT32);
child = (PyArrayObject *) PyArray_SimpleNew(1, &shape, NPY_INT32);
if (left == NULL || right == NULL || parent == NULL || child == NULL) {
goto out;
}
Py_BEGIN_ALLOW_THREADS