void test_bsp__tree_can_clip_tree(void) {
klist_t(poly) *polys = kl_init(poly);
float3 tr1[] = {{-0.2, 0.0, 0.0},
{0.2, 0.0, 0.0},
{0.0, 0.2, 0.0}};
float3 tr2[] = {{-0.2, 0.0, 100.0},
{0.2, 0.0, 100.0},
{0.0, 0.2, 1000.0}};
*kl_pushp(poly, polys) = poly_make_triangle(tr1[0], tr1[1], tr1[2]);
*kl_pushp(poly, polys) = poly_make_triangle(tr2[0], tr2[1], tr2[2]);
cl_assert_equal_i(polys->size, 2);
bsp_node_t *tr_bsp = bsp_build(NULL, polys, 1);
cl_assert(tr_bsp != NULL);
cl_assert(bsp_clip(tr_bsp, cube_bsp) != NULL);
klist_t(poly) *clipped = bsp_to_polygons(tr_bsp, 0, NULL);
cl_assert_equal_i(clipped->size, 1);
// Make sure we clipped the poly inside the cube, and kept
// the poly outside
float3 *v = &kl_val(kl_begin(clipped))->vertices[0];
cl_assert_((*v)[2] >= 99.0, "Should have kept the vertex outside the cube, not inside.");
kl_destroy(poly, polys);
}
void test_bsp__initialize(void) {
bsp = alloc_bsp_node();
poly_t *poly = NULL;
polygons = kl_init(poly);
float3 fs[] = {{-0.5, 0.0, 0.0},
{0.5, 0.0, 0.0},
{0.0, 0.5, 0.0}};
poly = poly_make_triangle(fs[0], fs[1], fs[2]);
cl_assert_(poly != NULL, "Out of memory");
*kl_pushp(poly, polygons) = poly;
float3 fs2[] = {{-0.5, 0.0, -0.5},
{0.5, 0.0, -0.5},
{0.0, 0.5, -0.5}};
poly = poly_make_triangle(fs2[0], fs2[1], fs2[2]);
cl_assert_(poly != NULL, "Out of memory");
*kl_pushp(poly, polygons) = poly;
float3 fs3[] = {{-0.5, 0.0, 0.5},
{0.5, 0.0, 0.5},
{0.0, 0.5, 0.5}};
poly = poly_make_triangle(fs3[0], fs3[1], fs3[2]);
cl_assert_(poly != NULL, "Out of memory");
*kl_pushp(poly, polygons) = poly;
float3 fs4[] = {{0.0, 0.0, -1.0},
{0.0, 0.0, 1.0},
{0.0, 1.0, 0.0}};
poly = poly_make_triangle(fs4[0], fs4[1], fs4[2]);
cl_assert_(poly != NULL, "Out of memory");
*kl_pushp(poly, polygons) = poly;
cl_assert_(bsp != NULL, "Out of memory");
cl_assert_(bsp_build(bsp, polygons, 1) != NULL, "Failed to build bsp tree");
stl_object *stl_cube = stl_read_file(cube_stl_file, 1);
cl_assert(stl_cube != NULL);
klist_t(poly) *cube_polys = kl_init(poly);
for(int i = 0; i < stl_cube->facet_count; i++) {
poly_t *p = poly_make_triangle(stl_cube->facets[i].vertices[0],
stl_cube->facets[i].vertices[1],
stl_cube->facets[i].vertices[2]);
cl_assert(p != NULL);
*kl_pushp(poly, cube_polys) = p;
}
cube_bsp = bsp_build(NULL, cube_polys, 1);
kl_destroy(poly, cube_polys);
cl_assert(cube_bsp != NULL);
}
void test_bsp__cube_bsp_can_return_poly_list_of_equal_length(void) {
// We test that when we get a list of polygons from a BSP tree of a cube
// and assert that we have the same number of polygons as when we started.
//
// A cube is nice here because no faces need to be split, so polygon
// counts before and after remain the same.
char cube_path[] = CLAR_FIXTURE_PATH "cube.stl";
stl_object *stl_cube = stl_read_file(cube_path, 0);
klist_t(poly) *cube_polys = kl_init(poly);
cl_assert(stl_cube != NULL);
cl_assert(stl_cube->facet_count > 0);
for(int i = 0; i < stl_cube->facet_count; i++) {
stl_facet *face = &stl_cube->facets[i];
poly_t *poly = poly_make_triangle(face->vertices[0], face->vertices[1], face->vertices[2]);
*kl_pushp(poly, cube_polys) = poly;
cl_assert(poly);
}
bsp_node_t *cube_bsp = alloc_bsp_node();
cl_assert(cube_bsp != NULL);
cl_assert(bsp_build(cube_bsp, cube_polys, 1) == cube_bsp);
klist_t(poly) *results = bsp_to_polygons(cube_bsp, 0, NULL);
cl_assert_equal_i(results->size, stl_cube->facet_count);
if(stl_cube) stl_free(stl_cube);
if(results) kl_destroy(poly, results);
kl_destroy(poly, cube_polys);
}
void test_bsp__tree_can_produce_triangles_from_quads(void) {
klist_t(poly) *quad = kl_init(poly);
// I'll make a quad by making a triangle with a missing
// vertex, then pushing the extra vertex after and recomputing
float3 quad_verts[] = {{-1.0, 1.0, 0.0},
{-1.0, -1.0, 0.0},
{1.0, -1.0, 0.0},
{1.0, 1.0, 0.0}};
poly_t *poly = poly_make_triangle(quad_verts[0], quad_verts[1], quad_verts[2]);
cl_assert_(poly != NULL, "Can't make triangle for test");
poly_push_vertex(poly, quad_verts[3]);
cl_assert_(poly_vertex_count(poly) == 4, "Failed to add vertex into quad");
poly_update(poly);
// Build a tree of the quad
klist_t(poly) *lpoly = kl_init(poly);
*kl_pushp(poly, lpoly) = poly;
bsp_node_t *quad_bsp = bsp_build(NULL, lpoly, 1);
cl_assert(quad_bsp);
klist_t(poly) *tris = bsp_to_polygons(quad_bsp, 1, NULL);
cl_assert_equal_i(tris->size, 2);
kl_destroy(poly, quad);
kl_destroy(poly, lpoly);
if(tris) kl_destroy(poly, tris);
}
bsp_node_t *clone_bsp_tree(bsp_node_t *tree) {
bsp_node_t *copy = alloc_bsp_node();
check_mem(copy);
kliter_t(poly) *iter = kl_begin(tree->polygons);
for(; iter != kl_end(tree->polygons); iter = kl_next(iter)) {
poly_t *poly_copy = clone_poly(kl_val(iter));
check_mem(poly_copy);
*kl_pushp(poly, copy->polygons) = poly_copy;
}
free_poly(copy->divider, 1);
if(tree->divider) {
copy->divider = clone_poly(tree->divider);
check_mem(copy->divider);
}
else {
copy->divider = NULL;
}
if(tree->front != NULL) {
copy->front = clone_bsp_tree(tree->front);
check_mem(copy->front);
}
if(tree->back != NULL) {
copy->back = clone_bsp_tree(tree->back);
check_mem(copy->back);
}
return copy;
error:
if(copy != NULL) free_bsp_tree(copy);
return NULL;
}
// Called when the manager sends a complete message
void messageArrivedFromManager() {
printf ("Message arrived: >%s< for >%s<\r\n", commandMessage, commandClientId);
// See if the client is connected, if so immediately forward
khiter_t k = kh_get(clientStatuses, clientStatuses, (char*)commandClientId); // Find it in the hash
if (k != kh_end(clientStatuses)) { // Was it in the hash?
clientStatus* status = kh_value(clientStatuses, k); // Grab the clientStatus from the hash
snprintf(httpResponse, HTTP_RESPONSE_SIZE, HTTP_TEMPLATE, commandMessageLen, commandMessage); // Compose the response message
write(status->io.fd, httpResponse, strlen(httpResponse)); // Send it
closeConnection((ev_io*)status); // Close the conn
return;
}
// If not, add to a queue
khiter_t q = kh_get(queue, queue, (char*)commandClientId); // See if this client is already in the queue
if (q == kh_end(queue)) {
printf("Creating queue for %s\r\n", commandClientId);
// This client needs to be added to the queue
// First make a new list
klist_t(messages) *newMessageList = kl_init(messages);
*kl_pushp(messages, newMessageList) = strdup((char*)commandMessage); // Add the message to the list
// Now make a new hash entry pointing to this new list
int ret;
q = kh_put(queue, queue, strdup((char*)commandClientId), &ret);
kh_value(queue, q) = newMessageList;
} else {
printf("Adding to the queue for %s\r\n", commandClientId);
// This client is in the queue already eg it has a hash entry
// Pushp puts this message at the end of the queue, so that shift will grab the oldest first (like a FIFO)
*kl_pushp(messages, kh_value(queue, q)) = strdup((char*)commandMessage);
}
// Now do a printout of the hash list
for (khiter_t qi = kh_begin(queue); qi < kh_end(queue); qi++) {
if (kh_exist(queue, qi)) {
printf("Queue for %s\n", kh_key(queue,qi));
klist_t(messages) *list = kh_value(queue, qi);
kliter_t(messages) *li;
for (li = kl_begin(list); li != kl_end(list); li = kl_next(li))
printf("%s\n", kl_val(li));
printf("----\n");
}
}
}
// Queue an event
void event_push(Event event, bool deferred)
{
// Sometimes libuv will run pending callbacks(timer for example) before
// blocking for a poll. If this happens and the callback pushes a event to one
// of the queues, the event would only be processed after the poll
// returns(user hits a key for example). To avoid this scenario, we call
// uv_stop when a event is enqueued.
uv_stop(uv_default_loop());
*kl_pushp(Event, deferred ? deferred_events : immediate_events) = event;
}
void test_polygon__initialize(void) {
faces = kl_init(poly);
// Set up three triangles, one on top of each other
// stored in list `faces` for easy cleanup
// and refferenced in `top` and `bottom`, and `square`
// used for inversion testing and area checking.
// And a square for non-triangular area tests and
float3 square_faces[] = {{0.0, 0.0, 0.0},
{1.0, 0.0, 0.0},
{1.0, 1.0, 0.0},
{0.0, 1.0, 0.0}};
square = alloc_poly();
cl_assert(square != NULL);
for(int i = 0; i < 3; i++) {
cl_assert_(poly_push_vertex(square, square_faces[i]),
"Failed to add square vertex");
}
cl_assert_equal_i(poly_vertex_count(square), 3);
*kl_pushp(poly, faces) = square;
// Set up a quad
quad = alloc_poly();
cl_assert(quad != NULL);
for(int i = 0; i < 4; i++) {
cl_assert_(poly_push_vertex(quad, square_faces[i]),
"Failed to add quad vertex.");
}
cl_assert_equal_i(poly_vertex_count(quad), 4);
*kl_pushp(poly, faces) = quad;
// Set up an invalid polygon which is just a line
line = alloc_poly();
cl_assert(line != NULL);
cl_assert(poly_push_vertex(line, square_faces[0]));
cl_assert(poly_push_vertex(line, square_faces[1]));
cl_assert(poly_push_vertex(line, square_faces[2]));
// Force the last vertex to be square_faces[0], then force a recompute
line->vertices[2][0] = line->vertices[0][0];
line->vertices[2][1] = line->vertices[0][1];
line->vertices[2][2] = line->vertices[0][2];
cl_assert(poly_update(line) == 0);
*kl_pushp(poly, faces) = line;
// Set up two triangles, one on top of each other
float3 fs[] = {{-0.5, 0.0, 0.0},
{0.5, 0.0, 0.0},
{0.0, 0.5, 0.0}};
bottom = poly_make_triangle(fs[0], fs[1], fs[2]);
cl_assert_(bottom != NULL, "Out of memory");
*kl_pushp(poly, faces) = bottom;
for(int i = 0; i < 3; i++) {
fs[i][2] += 1.0;
}
top = poly_make_triangle(fs[0], fs[1], fs[2]);
cl_assert_(top != NULL, "Out of memory");
*kl_pushp(poly, faces) = top;
cl_assert_equal_i(poly_classify_poly(top, bottom), BACK);
cl_assert_equal_i(poly_classify_poly(bottom, top), FRONT);
}
static void trans_tbl_init(bam_hdr_t* out, bam_hdr_t* translate, trans_tbl_t* tbl, bool merge_rg, bool merge_pg)
{
tbl->n_targets = translate->n_targets;
tbl->tid_trans = (int*)calloc(translate->n_targets, sizeof(int));
tbl->rg_trans = kh_init(c2c);
tbl->pg_trans = kh_init(c2c);
if (!tbl->tid_trans || !tbl->rg_trans || !tbl->pg_trans) { perror("out of memory"); exit(-1); }
int32_t out_len = out->l_text;
while (out_len > 0 && out->text[out_len-1] == '\n') {--out_len; } // strip trailing \n's
kstring_t out_text = { 0, 0, NULL };
kputsn(out->text, out_len, &out_text);
int i, min_tid = -1;
tbl->lost_coord_sort = false;
khash_t(c2i) *out_tid = kh_init(c2i);
for (i = 0; i < out->n_targets; ++i) {
int ret;
khiter_t iter = kh_put(c2i, out_tid, out->target_name[i], &ret);
if (ret <= 0) abort();
kh_value(out_tid, iter) = i;
}
for (i = 0; i < translate->n_targets; ++i) {
khiter_t iter = kh_get(c2i, out_tid, translate->target_name[i]);
if (iter == kh_end(out_tid)) { // Append missing entries to out
tbl->tid_trans[i] = out->n_targets++;
out->target_name = (char**)realloc(out->target_name, sizeof(char*)*out->n_targets);
out->target_name[out->n_targets-1] = strdup(translate->target_name[i]);
out->target_len = (uint32_t*)realloc(out->target_len, sizeof(uint32_t)*out->n_targets);
out->target_len[out->n_targets-1] = translate->target_len[i];
// grep line with regex '^@SQ.*\tSN:%s(\t.*$|$)', translate->target_name[i]
// from translate->text
regex_t sq_id;
regmatch_t* matches = (regmatch_t*)calloc(2, sizeof(regmatch_t));
if (matches == NULL) { perror("out of memory"); exit(-1); }
kstring_t seq_regex = { 0, 0, NULL };
ksprintf(&seq_regex, "^@SQ.*\tSN:%s(\t.*$|$)", translate->target_name[i]);
regcomp(&sq_id, seq_regex.s, REG_EXTENDED|REG_NEWLINE);
free(seq_regex.s);
if (regexec(&sq_id, translate->text, 1, matches, 0) != 0)
{
fprintf(pysamerr, "[trans_tbl_init] @SQ SN (%s) found in binary header but not text header.\n",translate->target_name[i]);
exit(1);
}
regfree(&sq_id);
// Produce our output line and append it to out_text
kputc('\n', &out_text);
kputsn(translate->text+matches[0].rm_so, matches[0].rm_eo-matches[0].rm_so, &out_text);
free(matches);
} else {
tbl->tid_trans[i] = kh_value(out_tid, iter);
}
if (tbl->tid_trans[i] > min_tid) {
min_tid = tbl->tid_trans[i];
} else {
tbl->lost_coord_sort = true;
}
}
kh_destroy(c2i, out_tid);
// grep @RG id's
regex_t rg_id;
regmatch_t* matches = (regmatch_t*)calloc(2, sizeof(regmatch_t));
if (matches == NULL) { perror("out of memory"); exit(-1); }
regcomp(&rg_id, "^@RG.*\tID:([!-)+-<>-~][ !-~]*)(\t.*$|$)", REG_EXTENDED|REG_NEWLINE);
char* text = translate->text;
klist_t(hdrln) *rg_list = kl_init(hdrln);
while(1) { // foreach rg id in translate's header
if (regexec(&rg_id, text, 2, matches, 0) != 0) break;
// matches[0] is the whole @RG line; matches[1] is the ID field value
kstring_t match_id = { 0, 0, NULL };
kputsn(text+matches[1].rm_so, matches[1].rm_eo-matches[1].rm_so, &match_id);
// is our matched ID in our output list already
regex_t rg_id_search;
kstring_t rg_regex = { 0, 0, NULL };
ksprintf(&rg_regex, "^@RG.*\tID:%s(\t.*$|$)", match_id.s);
regcomp(&rg_id_search, rg_regex.s, REG_EXTENDED|REG_NEWLINE|REG_NOSUB);
free(rg_regex.s);
kstring_t transformed_id = { 0, 0, NULL };
bool transformed_equals_match;
if (regexec(&rg_id_search, out->text, 0, NULL, 0) != 0 || merge_rg) {
// Not in there so can add it as 1-1 mapping
kputs(match_id.s, &transformed_id);
transformed_equals_match = true;
} else {
// It's in there so we need to transform it by appending random number to id
ksprintf(&transformed_id, "%s-%0lX", match_id.s, lrand48());
transformed_equals_match = false;
}
regfree(&rg_id_search);
// Insert it into our translation map
int in_there = 0;
khiter_t iter = kh_put(c2c, tbl->rg_trans, ks_release(&match_id), &in_there);
char *transformed_id_s = ks_release(&transformed_id);
kh_value(tbl->rg_trans,iter) = transformed_id_s;
// take matched line and replace ID with transformed_id
kstring_t transformed_line = { 0, 0, NULL };
if (transformed_equals_match) {
kputsn(text+matches[0].rm_so, matches[0].rm_eo-matches[0].rm_so, &transformed_line);
} else {
kputsn(text+matches[0].rm_so, matches[1].rm_so-matches[0].rm_so, &transformed_line);
kputs(transformed_id_s, &transformed_line);
kputsn(text+matches[1].rm_eo, matches[0].rm_eo-matches[1].rm_eo, &transformed_line);
}
if (!(transformed_equals_match && merge_rg)) {
// append line to linked list for PG processing
char** ln = kl_pushp(hdrln, rg_list);
*ln = ks_release(&transformed_line); // Give away to linked list
}
else free(transformed_line.s);
text += matches[0].rm_eo; // next!
}
regfree(&rg_id);
// Do same for PG id's
regex_t pg_id;
regcomp(&pg_id, "^@PG.*\tID:([!-)+-<>-~][ !-~]*)(\t.*$|$)", REG_EXTENDED|REG_NEWLINE);
text = translate->text;
klist_t(hdrln) *pg_list = kl_init(hdrln);
while(1) { // foreach pg id in translate's header
if (regexec(&pg_id, text, 2, matches, 0) != 0) break;
kstring_t match_id = { 0, 0, NULL };
kputsn(text+matches[1].rm_so, matches[1].rm_eo-matches[1].rm_so, &match_id);
// is our matched ID in our output list already
regex_t pg_id_search;
kstring_t pg_regex = { 0, 0, NULL };
ksprintf(&pg_regex, "^@PG.*\tID:%s(\t.*$|$)", match_id.s);
regcomp(&pg_id_search, pg_regex.s, REG_EXTENDED|REG_NEWLINE|REG_NOSUB);
free(pg_regex.s);
kstring_t transformed_id = { 0, 0, NULL };
bool transformed_equals_match;
if (regexec(&pg_id_search, out->text, 0, NULL, 0) != 0 || merge_pg) {
// Not in there so can add it as 1-1 mapping
kputs(match_id.s, &transformed_id);
transformed_equals_match = true;
} else {
// It's in there so we need to transform it by appending random number to id
ksprintf(&transformed_id, "%s-%0lX", match_id.s, lrand48());
transformed_equals_match = false;
}
regfree(&pg_id_search);
// Insert it into our translation map
int in_there = 0;
khiter_t iter = kh_put(c2c, tbl->pg_trans, ks_release(&match_id), &in_there);
char *transformed_id_s = ks_release(&transformed_id);
kh_value(tbl->pg_trans,iter) = transformed_id_s;
// take matched line and replace ID with transformed_id
kstring_t transformed_line = { 0, 0, NULL };
if (transformed_equals_match) {
kputsn(text+matches[0].rm_so, matches[0].rm_eo-matches[0].rm_so, &transformed_line);
} else {
kputsn(text+matches[0].rm_so, matches[1].rm_so-matches[0].rm_so, &transformed_line);
kputs(transformed_id_s, &transformed_line);
kputsn(text+matches[1].rm_eo, matches[0].rm_eo-matches[1].rm_eo, &transformed_line);
}
if (!(transformed_equals_match && merge_pg)) {
// append line to linked list for PP processing
char** ln = kl_pushp(hdrln, pg_list);
*ln = ks_release(&transformed_line); // Give away to linked list
}
else free(transformed_line.s);
text += matches[0].rm_eo; // next!
}
regfree(&pg_id);
// need to translate PP's on the fly in second pass because they may not be in correct order and need complete tbl->pg_trans to do this
// for each line {
// with ID replaced with tranformed_id and PP's transformed using the translation table
// }
regex_t pg_pp;
regcomp(&pg_pp, "^@PG.*\tPP:([!-)+-<>-~][!-~]*)(\t.*$|$)", REG_EXTENDED|REG_NEWLINE);
kliter_t(hdrln) *iter = kl_begin(pg_list);
while (iter != kl_end(pg_list)) {
char* data = kl_val(iter);
kstring_t transformed_line = { 0, 0, NULL };
// Find PP tag
if (regexec(&pg_pp, data, 2, matches, 0) == 0) {
// Lookup in hash table
kstring_t pp_id = { 0, 0, NULL };
kputsn(data+matches[1].rm_so, matches[1].rm_eo-matches[1].rm_so, &pp_id);
khiter_t k = kh_get(c2c, tbl->pg_trans, pp_id.s);
free(pp_id.s);
char* transformed_id = kh_value(tbl->pg_trans,k);
// Replace
kputsn(data, matches[1].rm_so-matches[0].rm_so, &transformed_line);
kputs(transformed_id, &transformed_line);
kputsn(data+matches[1].rm_eo, matches[0].rm_eo-matches[1].rm_eo, &transformed_line);
} else { kputs(data, &transformed_line); }
// Produce our output line and append it to out_text
kputc('\n', &out_text);
kputsn(transformed_line.s, transformed_line.l, &out_text);
free(transformed_line.s);
free(data);
iter = kl_next(iter);
}
regfree(&pg_pp);
// Need to also translate @RG PG's on the fly too
regex_t rg_pg;
regcomp(&rg_pg, "^@RG.*\tPG:([!-)+-<>-~][!-~]*)(\t.*$|$)", REG_EXTENDED|REG_NEWLINE);
kliter_t(hdrln) *rg_iter = kl_begin(rg_list);
while (rg_iter != kl_end(rg_list)) {
char* data = kl_val(rg_iter);
kstring_t transformed_line = { 0, 0, NULL };
// Find PG tag
if (regexec(&rg_pg, data, 2, matches, 0) == 0) {
// Lookup in hash table
kstring_t pg_id = { 0, 0, NULL };
kputsn(data+matches[1].rm_so, matches[1].rm_eo-matches[1].rm_so, &pg_id);
khiter_t k = kh_get(c2c, tbl->pg_trans, pg_id.s);
free(pg_id.s);
char* transformed_id = kh_value(tbl->pg_trans,k);
// Replace
kputsn(data, matches[1].rm_so-matches[0].rm_so, &transformed_line);
kputs(transformed_id, &transformed_line);
kputsn(data+matches[1].rm_eo, matches[0].rm_eo-matches[1].rm_eo, &transformed_line);
} else { kputs(data, &transformed_line); }
// Produce our output line and append it to out_text
kputc('\n', &out_text);
kputsn(transformed_line.s, transformed_line.l, &out_text);
free(transformed_line.s);
free(data);
rg_iter = kl_next(rg_iter);
}
regfree(&rg_pg);
kl_destroy(hdrln,pg_list);
kl_destroy(hdrln,rg_list);
free(matches);
// Add trailing \n and write back to header
free(out->text);
kputc('\n', &out_text);
out->l_text = out_text.l;
out->text = ks_release(&out_text);
}
// Push an event to the queue
void event_push(Event event)
{
*kl_pushp(Event, event_queue) = event;
}
