sgtlib 3.3.9b0__py3-none-any.whl → 3.4.0__py3-none-any.whl

StructuralGT/__init__.py

@@ -24,7 +24,7 @@ of the GNU General Public License along with this program.  If not, see <https:/
 
 
 # Project Details
-__version__ = "3.3.9beta"
+__version__ = "3.4.0"
 __install_version__ = "3.3.9"
 __title__ = f"StructuralGT (v{__version__})"
 __author__ = "Dickson Owuor"

StructuralGT/compute/c_lang/sgt_base.c

@@ -0,0 +1,61 @@
+//#define _POSIX_C_SOURCE 200809L  // Linux
+#include <stdio.h>
+#include <stdarg.h>
+#include <string.h>
+//#include "sgt_base.h"
+#include "include/sgt_base.h"
+
+// Function to compute Local Node Connectivity
+void* compute_lnc(void *arg) {
+    ThreadArgsLNC *args = (ThreadArgsLNC*)arg;
+    igraph_integer_t lnc;
+
+    igraph_st_vertex_connectivity(args->graph, &lnc, args->i, args->j, IGRAPH_VCONN_NEI_NEGATIVE);
+
+    // Update shared data under mutex lock
+    pthread_mutex_lock(args->mutex);
+    if (lnc != -1){
+        *(args->total_nc) += lnc;
+        *(args->total_count) += 1;
+        //printf("got %d\n", lnc);
+        //printf("NC:%d Count:%d \n", *(args->total_nc), *(args->total_count));
+    }
+    pthread_mutex_unlock(args->mutex);
+    
+    pthread_exit(NULL);
+}
+
+// Function to convert string representation of adjacency matrix to 2D matrix
+igraph_matrix_t* str_to_matrix(char* str_adj_mat, igraph_integer_t num_vertices) {
+    // Allocate memory for the matrix
+    igraph_matrix_t* mat = (igraph_matrix_t*)malloc(sizeof(igraph_matrix_t));
+    if (!mat) {
+        fprintf(stderr, "Failed to allocate memory for matrix structure\n");
+        exit(EXIT_FAILURE);
+    }
+    igraph_matrix_init(mat, num_vertices, num_vertices);
+
+    // Parse string and populate matrix
+    char* token;
+    char* nextToken;
+    const char delimiters[] = ",";
+
+    // Get the first token
+    // strtok_r - MacOs
+    //token = strtok_r(str_adj_mat, delimiters, &nextToken);
+    token = strtok_s(str_adj_mat, delimiters, &nextToken);
+
+    // Iterate through the remaining tokens
+    for (igraph_integer_t i = 0; i < num_vertices; i++) {
+        for (igraph_integer_t j = 0; j < num_vertices; j++) {
+            MATRIX(*mat, i, j) = atoi(token);
+            // Get the next token
+            // strtok_r - MacOs
+            //token = strtok_r(NULL, delimiters, &nextToken);
+            token = strtok_s(NULL, delimiters, &nextToken);
+        }
+    }
+
+    return mat;
+}
+

StructuralGT/compute/c_lang/sgtmodule.c

@@ -0,0 +1,183 @@
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdarg.h>
+
+#define PY_SSIZE_T_CLEAN
+#include <Python.h>
+//#include "sgt_base.h"
+#include "include/sgt_base.h"
+
+
+static PyObject *ErrorObject;
+static PyObject *
+compute_anc(PyObject *self, PyObject *args)
+{
+    int num_cpus;
+    int allow_mp;
+    char *f_name;
+
+    // Consider passing graph as String
+    if (!PyArg_ParseTuple(args, "sii:compute_anc", &f_name, &num_cpus, &allow_mp)){
+        return NULL;
+    }
+
+	/*if ( f_name == ''){
+    	PyErr_SetString(ErrorObject, "Unable to retrieve graph.");
+    	return NULL;
+  	}*/
+
+	if ( num_cpus <= 0 || allow_mp < 0){
+    	PyErr_SetString(ErrorObject, "Invalid CPU parameters.");
+    	return NULL;
+  	}
+
+    // Declare required variables
+  	FILE *file;
+
+  	igraph_t graph;
+	igraph_integer_t num_nodes;
+    igraph_integer_t count_nc = 0;
+    igraph_integer_t sum_nc = 0;
+    igraph_real_t anc = 0;
+
+    // Open the file containing the serialized graph
+    file = fopen(f_name, "r");
+    // Read the graph from the file
+    igraph_read_graph_edgelist(&graph, file, 0, IGRAPH_UNDIRECTED);
+    fclose(file);
+    // printf("Nodes: %d\nEdges: %d\n", (int)igraph_vcount(&graph), (int)igraph_ecount(&graph));
+
+	num_nodes = igraph_vcount(&graph);
+	if (allow_mp == 0){
+        printf("Using single processing\n");
+        igraph_integer_t lnc;
+        for (igraph_integer_t i=0; i<num_nodes; i++) {
+            for (igraph_integer_t j=i+1; j<num_nodes; j++){
+                igraph_st_vertex_connectivity(&graph, &lnc, i, j, IGRAPH_VCONN_NEI_NEGATIVE);
+                if (lnc == -1) { continue; }
+                sum_nc += lnc;
+                count_nc += 1;
+            }
+        }
+
+    }
+    else {
+        printf("Using multiprocessing\n");
+        // Initialize mutex
+        pthread_mutex_t mutex;
+        pthread_mutex_init(&mutex, NULL);
+
+        // Create thread pool
+        const int MAX_THREAD_COUNT = num_cpus;
+
+        // Allocate memory for threads and args arrays
+        pthread_t *threads = (pthread_t *)malloc(MAX_THREAD_COUNT * sizeof(pthread_t));
+        ThreadArgsLNC *args = (ThreadArgsLNC *)malloc(MAX_THREAD_COUNT * sizeof(ThreadArgsLNC));
+
+        if (threads == NULL || args == NULL) {
+            PyErr_SetString(ErrorObject, "Memory allocation failed\n");
+    	    return NULL;
+        }
+
+        // Initialize thread pool
+        for (int i = 0; i < MAX_THREAD_COUNT; i++) {
+            args[i].graph = &graph;
+            args[i].mutex = &mutex;
+            args[i].total_nc = &sum_nc;
+            args[i].total_count = &count_nc;
+        }
+
+        // Create threads for computing LNC
+        int idx = 0;
+        int thread_count = 0;
+        for (igraph_integer_t i = 0; i < num_nodes; i++) {
+            for (igraph_integer_t j = i + 1; j < num_nodes; j++) {
+                idx = (int)(thread_count % MAX_THREAD_COUNT);
+                if (thread_count >= MAX_THREAD_COUNT) {
+                    // Wait for a thread to finish before starting a new one
+                    pthread_join(threads[idx], NULL);
+                    thread_count++;
+                }
+                args[idx].i = (int)i;
+                args[idx].j = (int)j;
+                pthread_create(&threads[idx], NULL, compute_lnc, &args[idx]);
+                thread_count++;
+                // printf("thread %d running...\n", (idx));
+            }
+        }
+
+        // Join threads
+        for (int i = 0; i < MAX_THREAD_COUNT && i < thread_count; i++) {
+            pthread_join(threads[i], NULL);
+        }
+
+        // Destroy mutex
+        pthread_mutex_destroy(&mutex);
+        // Free dynamically allocated memory
+        free(threads);
+        free(args);
+    }
+
+    // Compute ANC
+    anc = (float) sum_nc / count_nc;
+
+    // Destroy graph
+    igraph_destroy(&graph);
+
+    return PyFloat_FromDouble((double) anc);
+
+}
+static char compute_anc_doc[] =
+"A C method that uses iGraph library to compute average node connectivity of a graph.\n"
+"\n"
+"Args:\n"
+"   file (string): CSV file with edge list of graph A.\n"
+"   cpus (int): number of available CPUs.\n"
+"   mp (int): allow multi-processing (0: No, 1: Yes).\n"
+"\n"
+"Returns:\n"
+"   ANC (float): Average Node Connectivity as a float value.\n";
+
+
+static char sgt_doc[] =
+"A C language module leveraging the iGraph library to compute Graph Theory (GT) metrics,"
+"enhanced with multi-threading capabilities for accelerated computation.\n";
+
+/* Method Table: ist of functions defined in the module */
+static PyMethodDef sgt_methods[] = {
+    {"compute_anc", compute_anc, METH_VARARGS, compute_anc_doc },
+    //{"compute_lnc", compute_lnc, METH_VARARGS, "Compute local node connectivity." },
+	{NULL, NULL, 0, NULL}        /* Sentinel */
+};
+
+/* Create module */
+static struct PyModuleDef sgt_c_module = {
+    PyModuleDef_HEAD_INIT,
+    "sgt_c_module",   /* name of module */
+    sgt_doc, /* module documentation, may be NULL */
+    -1,       /* size of per-interpreter state of the module, or -1 if the module keeps state in global variables. */
+    sgt_methods
+};
+
+/* Initialization function for the module */
+PyMODINIT_FUNC
+PyInit_sgt_c_module(void)
+{
+    PyObject *m;
+
+    m = PyModule_Create(&sgt_c_module);
+    if (m == NULL)
+        return NULL;
+
+    ErrorObject = PyErr_NewException("sgt_c_module.error", NULL, NULL);
+    Py_XINCREF(ErrorObject);
+    if (PyModule_AddObject(m, "error", ErrorObject) < 0) {
+        Py_XDECREF(ErrorObject);
+        Py_CLEAR(ErrorObject);
+        Py_DECREF(m);
+        return NULL;
+    }
+
+    return m;
+}
+

StructuralGT/compute/graph_analyzer.py

@@ -29,7 +29,6 @@ from networkx.algorithms.flow import maximum_flow
 from networkx.algorithms.distance_measures import diameter, periphery
 from networkx.algorithms.wiener import wiener_index
 
-from .c_lang import sgt_c_module as sgt
 from ..utils.progress_update import ProgressUpdate
 from ..networks.fiber_network import FiberNetworkBuilder
 from ..imaging.image_processor import ImageProcessor
@@ -654,6 +653,7 @@ class GraphAnalyzer(ProgressUpdate):
         ---------
         :param nx_graph: NetworkX graph object.
         """
+        from .c_lang import sgt_c_module as sgt
 
         cpu_count = get_num_cores()
         num_threads = cpu_count if nx.number_of_nodes(nx_graph) < 2000 else cpu_count * 2

{sgtlib-3.3.9b0.dist-info → sgtlib-3.4.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sgtlib
-Version: 3.3.9b0
+Version: 3.4.0
 Summary: A software tool for graph theory analysis of microscopy images.
 Author-email: Dickson Owuor <owuordickson@gmail.com>, "Drew A. Vecchio" <vecdrew@umich.edu>, Kody Whisnant <kgwhis@umich.edu>, Alain Kadar <alaink@umich.edu>, Xiong Ye Xiao <xiongyex@usc.edu>, Nicholas Kotov <kotov@umich.edu>
 Maintainer-email: Dickson Owuor <owuordickson@gmail.com>

{sgtlib-3.3.9b0.dist-info → sgtlib-3.4.0.dist-info}/RECORD

@@ -1,4 +1,4 @@
-StructuralGT/__init__.py,sha256=rVWsQlTc1X6aXvaoHEdLGtaLWpcu2EtFD4ZszbYJtbg,1258
+StructuralGT/__init__.py,sha256=8O4pI5ydEdxVMuojfGLzMWBjt7dVw2shSmAmw52F9tg,1254
 StructuralGT/entrypoints.py,sha256=s2upsOVsy9zsoorxiZXaZKiLw7fUOQwHjwup3C089Hs,1413
 StructuralGT/modules.py,sha256=CYudBMwP70cRFWj_Dppr_Kdc08V_-9wWKVd48bEHkS0,743
 StructuralGT/apps/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -50,7 +50,9 @@ StructuralGT/apps/sgt_qml/widgets/RescaleControlWidget.qml,sha256=qb6fXok5C1HJjb
 StructuralGT/apps/sgt_qml/widgets/RibbonWidget.qml,sha256=POaPwXh7vE4UwU82x-80BuI2625FLWbmJQsZliy618w,13990
 StructuralGT/apps/sgt_qml/widgets/StatusBarWidget.qml,sha256=YRTSg_4aYA3FO69wT1NnX0Ri_qRx3AHhVrS1n3pVwd4,5969
 StructuralGT/compute/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-StructuralGT/compute/graph_analyzer.py,sha256=zQ8qZSeGysU3ubIvOPKMQlSTmUxdRoENa_lV4jpDxE4,69851
+StructuralGT/compute/graph_analyzer.py,sha256=E2vIaIcApy3VI7gM2rLZ30X8SGtOhzhEkVufMcL-ngA,69859
+StructuralGT/compute/c_lang/sgt_base.c,sha256=VFgwVDALjWl_zAP5NqNwG5pLv6no91_93RYPziHT2hY,1953
+StructuralGT/compute/c_lang/sgtmodule.c,sha256=85VhQCxNow49yslayaCnCFwseS6vXVvJ77RjypkHG1o,5492
 StructuralGT/compute/c_lang/include/sgt_base.h,sha256=jkCpNy_01bSKk_ay6_1TilNhribMmw-p8r8FRhamstM,530
 StructuralGT/imaging/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 StructuralGT/imaging/base_image.py,sha256=Cc4xeVOxpID6SukVolYtD6OiEQ4tsUGQ4mYjE3QF_2E,16555
@@ -64,9 +66,9 @@ StructuralGT/utils/config_loader.py,sha256=8px8iGOFCGz8qIZCfyGuAFfvvaVdOjogf9PqS
 StructuralGT/utils/configs.ini,sha256=sKPsAd15_YubgGhLMVuse1JRuU7S6bFYjLbzkuoD5JI,2326
 StructuralGT/utils/progress_update.py,sha256=9X_9mGLgTMF5dDSTNKpELQcmFv8r1wz6YZQCqy4tCl8,1621
 StructuralGT/utils/sgt_utils.py,sha256=0vg7I4P6PIao_H8-KYgkCJ6TM9eESW-RwGZB4sGgCI4,9109
-sgtlib-3.3.9b0.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-sgtlib-3.3.9b0.dist-info/METADATA,sha256=LhSgnFTCv66a-Yd0lSiQhed0qgpmGDWkK0T-U404VMQ,45280
-sgtlib-3.3.9b0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-sgtlib-3.3.9b0.dist-info/entry_points.txt,sha256=zY3v_U9Qi4L965BPrURXn84yF_TxdKDZI3VcTUbTh0M,120
-sgtlib-3.3.9b0.dist-info/top_level.txt,sha256=daVVcqfvgGeWXFnHArFOFbRmtWxL93fxmZjF19Sg69I,13
-sgtlib-3.3.9b0.dist-info/RECORD,,
+sgtlib-3.4.0.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+sgtlib-3.4.0.dist-info/METADATA,sha256=KLud3ApS4KMRC6hYaHiseM1P4kQ57Oy8EhNvQ9B9ANU,45278
+sgtlib-3.4.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+sgtlib-3.4.0.dist-info/entry_points.txt,sha256=zY3v_U9Qi4L965BPrURXn84yF_TxdKDZI3VcTUbTh0M,120
+sgtlib-3.4.0.dist-info/top_level.txt,sha256=daVVcqfvgGeWXFnHArFOFbRmtWxL93fxmZjF19Sg69I,13
+sgtlib-3.4.0.dist-info/RECORD,,