sgtlib 3.3.9__py3-none-any.whl

StructuralGT/utils/config_loader.py

@@ -0,0 +1,244 @@
+# SPDX-License-Identifier: GNU GPL v3
+
+"""
+Loads default configurations from 'configs.ini' file
+"""
+
+import os
+import configparser
+from typing import Union
+
+from .sgt_utils import verify_path
+
+
+def strict_read_config_file(config_path, update_func=None):
+    """
+    Strictly read the contents of the 'configs.ini' file, otherwise stop execution.
+
+    Args:
+        config_path (str): path to config file
+        update_func (function): function that will be called to give message updates
+
+    Returns:
+        ConfigParser object or None if an error occurs.
+    """
+    success, result = verify_path(config_path)
+    if not success:
+        if update_func is not None:
+            update_func(-1, f"File Error: unable to find config file {config_path}.")
+        return False
+
+    config = configparser.ConfigParser()
+    config_file = result
+    try:
+        config.read(config_file)
+        return True
+    except configparser.Error:
+        if update_func is not None:
+            update_func(-1, f"Unable to read the configs from {config_file}.")
+        return False
+
+
+def read_config_file(config_path):
+    """Read the contents of the 'configs.ini' file"""
+    config = configparser.ConfigParser()
+    success, result = verify_path(config_path)
+    if success:
+        config_file = result
+    else:
+        # print(f"File Error: unable to find config file {config_path}. Using the default config file")
+        # Get the directory of the current script
+        script_dir = os.path.dirname(os.path.abspath(__file__))
+        config_path = 'configs.ini'
+        config_file = os.path.join(script_dir, config_path)
+    # Load the default configuration from the file
+    try:
+        config.read(config_file)
+        return config
+    except configparser.Error:
+        # print(f"Unable to read the configs from {config_file}.")
+        return None
+
+
+def load_img_configs(cfg_path: str = ""):
+    """Image Detection settings"""
+
+    options_img: dict[str, dict[str, Union[int, float]]] = {
+        "threshold_type": {"id": "threshold_type", "type": "binary-filter", "text": "", "visible": 1, "value": 0 },
+        "global_threshold_value": {"id": "global_threshold_value", "type": "binary-filter", "text": "", "visible": 1, "value": 128 },
+        "adaptive_local_threshold_value": {"id": "adaptive_local_threshold_value", "type": "binary-filter", "text": "", "visible": 1, "value": 11 },
+        "otsu": {"id": "otsu", "type": "binary-filter", "text": "", "visible": 0, "value": 0},
+        "apply_dark_foreground": {"id": "apply_dark_foreground", "type": "binary-filter", "text": "", "visible": 1, "value": 0},
+
+        "apply_autolevel": {"id": "apply_autolevel", "type": "image-filter", "text": "Autolevel", "value": 0,
+                            "dataId": "autolevel_blurring_size", "dataValue": 3, "minValue": 1, "maxValue": 7, "stepSize": 2},
+        "apply_gaussian_blur": {"id": "apply_gaussian_blur", "type": "image-filter", "text": "Gaussian", "value": 0,
+                                "dataId": "gaussian_blurring_size", "dataValue": 3, "minValue": 1, "maxValue": 7, "stepSize": 2 },
+        "apply_laplacian_gradient": {"id": "apply_laplacian_gradient", "type": "image-filter", "text": "Laplacian",
+                                     "value": 0, "dataId": "laplacian_kernel_size", "dataValue": 3, "minValue": 1, "maxValue": 7,  "stepSize": 2 },
+        "apply_lowpass_filter": {"id": "apply_lowpass_filter", "type": "image-filter", "text": "Lowpass", "value": 0,
+                                 "dataId": "lowpass_window_size", "dataValue": 10, "minValue": 0, "maxValue": 1000,  "stepSize": 1 },
+        "apply_gamma": {"id": "apply_gamma", "type": "image-filter", "text": "LUT Gamma", "value": 1, "dataId": "adjust_gamma",
+                        "dataValue": 1.0, "minValue": 0.01, "maxValue": 5.0, "stepSize": 0.01  },
+        "apply_sobel_gradient": {"id": "apply_sobel_gradient", "type": "image-filter", "text": "Sobel", "value": 0,
+                                 "dataId": "sobel_kernel_size", "dataValue": 3, "minValue": 1, "maxValue": 7,  "stepSize": 2 },
+        "apply_median_filter": {"id": "apply_median_filter", "type": "image-filter", "text": "Median", "value": 0 },
+        "apply_scharr_gradient": {"id": "apply_scharr_gradient", "type": "image-filter", "text": "Scharr", "value": 0},
+
+        "brightness_level": {"id": "brightness_level", "type": "image-control", "text": "Brightness", "value": 0 },
+        "contrast_level": {"id": "contrast_level", "type": "image-control", "text": "Contrast", "value": 0 },
+
+        "scale_value_nanometers": {"id": "scale_value_nanometers", "type": "image-property", "text": "Scalebar (nm)", "visible": 1, "value": 0.0 },
+        "scalebar_pixel_count": {"id": "scalebar_pixel_count", "type": "image-property", "text": "Scalebar Pixel Count", "visible": 1, "value": 1 },
+        "resistivity": {"id": "resistivity", "type": "image-property", "text": "Resistivity (<html>&Omega;</html>m)", "visible": 1, "value": 1.0 },
+        "pixel_width": {"id": "pixel_width", "type": "image-property", "text": "", "visible": 0, "value": 1.0},  # * (10**-9)  # 1 nanometer
+
+        "save_images": {"id": "save_images", "type": "file-options", "text": "Save All Images", "visible": 1, "value": 0},
+    }
+
+    # Load configuration from the file
+    config = read_config_file(cfg_path)
+    if config is None:
+        return options_img
+
+    try:
+        options_img["threshold_type"]["value"] = int(config.get('filter-settings', 'threshold_type'))
+        options_img["global_threshold_value"]["value"] = int(config.get('filter-settings', 'global_threshold_value'))
+        options_img["adaptive_local_threshold_value"]["value"] = int(config.get('filter-settings', 'adaptive_local_threshold_value'))
+        options_img["apply_dark_foreground"]["value"] = int(config.get('filter-settings', 'apply_dark_foreground'))
+
+        options_img["apply_gamma"]["value"] = int(config.get('filter-settings', 'apply_gamma'))
+        options_img["apply_gamma"]["dataValue"] = float(config.get('filter-settings', 'adjust_gamma'))
+        options_img["apply_autolevel"]["value"] = int(config.get('filter-settings', 'apply_autolevel'))
+        options_img["apply_autolevel"]["dataValue"] = int(config.get('filter-settings', 'blurring_window_size'))
+        options_img["apply_laplacian_gradient"]["value"] = int(config.get('filter-settings', 'apply_laplacian_gradient'))
+        options_img["apply_laplacian_gradient"]["dataValue"] = 3
+        options_img["apply_sobel_gradient"]["value"] = int(config.get('filter-settings', 'apply_sobel_gradient'))
+        options_img["apply_sobel_gradient"]["dataValue"] = 3
+        options_img["apply_gaussian_blur"]["value"] = int(config.get('filter-settings', 'apply_gaussian_blur'))
+        options_img["apply_gaussian_blur"]["dataValue"] = int(config.get('filter-settings', 'blurring_window_size'))
+        options_img["apply_lowpass_filter"]["value"] = int(config.get('filter-settings', 'apply_lowpass_filter'))
+        options_img["apply_lowpass_filter"]["dataValue"] = int(config.get('filter-settings', 'filter_window_size'))
+
+        options_img["apply_scharr_gradient"]["value"] = int(config.get('filter-settings', 'apply_scharr_gradient'))
+        options_img["apply_median_filter"]["value"] = int(config.get('filter-settings', 'apply_median_filter'))
+
+        options_img["brightness_level"]["value"] = int(config.get('filter-settings', 'brightness_level'))
+        options_img["contrast_level"]["value"] = int(config.get('filter-settings', 'contrast_level'))
+        options_img["scale_value_nanometers"]["value"] = float(config.get('filter-settings', 'scale_value_nanometers'))
+        options_img["scalebar_pixel_count"]["value"] = int(config.get('filter-settings', 'scalebar_pixel_count'))
+        options_img["resistivity"]["value"] = float(config.get('filter-settings', 'resistivity'))
+
+        options_img["save_images"]["value"] = int(config.get('file-options', 'save_images'))
+
+        return options_img
+    except configparser.NoSectionError:
+        return options_img
+
+
+def load_gte_configs(cfg_path: str = ""):
+    """Graph Extraction Settings"""
+
+    options_gte = {
+        "has_weights": {"id": "has_weights", "type": "graph-extraction", "text": "Add Weights", "value": 0,
+                        "items": [
+                            {"id": "DIA", "text": "by diameter", "value": 1},
+                            {"id": "AREA", "text": "by area", "value": 0},
+                            {"id": "LEN", "text": "by length", "value": 0},
+                            {"id": "ANGLE", "text": "by angle", "value": 0},
+                            {"id": "INV-LEN", "text": "by inverse-length", "value": 0},
+                            {"id": "FIX-CON", "text": "by conductance", "value": 0},
+                            {"id": "RES", "text": "by resistance", "value": 0},
+                        ]},
+        "merge_nearby_nodes": {"id": "merge_nearby_nodes", "type": "graph-extraction", "text": "Merge Nearby Nodes", "value": 1, "items": [{"id": "merge_node_radius_size", "text": "", "value": 2}]},
+        "prune_dangling_edges": {"id": "prune_dangling_edges", "type": "graph-extraction", "text": "Prune Dangling Edges", "value": 1, "items": [{"id": "prune_max_iteration_count", "text": "", "value": 500}]},
+        "remove_disconnected_segments": {"id": "remove_disconnected_segments", "type": "graph-extraction", "text": "Remove Disconn. Segments", "value": 1, "items": [{"id": "remove_object_size", "text": "", "value": 500}]},
+        "remove_self_loops": {"id": "remove_self_loops", "type": "graph-extraction", "text": "Remove Self Loops", "value": 1},
+        "display_node_id": {"id": "display_node_id", "type": "graph-extraction", "text": "Display Node ID", "value": 0},
+
+        "export_edge_list": {"id": "export_edge_list", "type": "file-options", "text": "Export Edge List", "value": 0},
+        "export_as_gexf": {"id": "export_as_gexf", "type": "file-options", "text": "Export as gexf", "value": 0},
+        "export_adj_mat": {"id": "export_adj_mat", "type": "file-options", "text": "Export Adjacency Matrix", "value": 0},
+        "export_as_gsd": {"id": "export_as_gsd", "type": "file-options", "text": "Export as GSD/HOOMD", "value": 0},
+    }
+
+    # Load configuration from the file
+    config = read_config_file(cfg_path)
+    if config is None:
+        return options_gte
+
+    try:
+
+        options_gte["merge_nearby_nodes"]["value"] = int(config.get('extraction-settings', 'merge_nearby_nodes'))
+        options_gte["merge_nearby_nodes"]["items"][0]["value"] = int(
+            config.get('extraction-settings', 'merge_node_radius_size'))
+        options_gte["prune_dangling_edges"]["value"] = int(config.get('extraction-settings', 'prune_dangling_edges'))
+        options_gte["prune_dangling_edges"]["items"][0]["value"] = int(
+            config.get('extraction-settings', 'prune_max_iteration_count'))
+        options_gte["remove_disconnected_segments"]["value"] = int(
+            config.get('extraction-settings', 'remove_disconnected_segments'))
+        options_gte["remove_disconnected_segments"]["items"][0]["value"] = int(config.get('extraction-settings', 'remove_object_size'))
+        options_gte["remove_self_loops"]["value"] = int(config.get('extraction-settings', 'remove_self_loops'))
+        options_gte["has_weights"]["value"] = int(config.get('extraction-settings', 'add_weights'))
+        weight_type = str(config.get('extraction-settings', 'weight_type'))
+        for i in range(len(options_gte["has_weights"]["items"])):
+            options_gte["has_weights"]["items"][i]["value"] = 1 if options_gte["has_weights"]["items"][i]["id"] == weight_type else 0
+        options_gte["display_node_id"]["value"] = int(config.get('extraction-settings', 'display_node_id'))
+        options_gte["export_edge_list"]["value"] = int(config.get('extraction-settings', 'export_edge_list'))
+        options_gte["export_as_gexf"]["value"] = int(config.get('extraction-settings', 'export_as_gexf'))
+        options_gte["export_adj_mat"]["value"] = int(config.get('extraction-settings', 'export_adj_mat'))
+        options_gte["export_as_gsd"]["value"] = int(config.get('extraction-settings', 'export_as_gsd'))
+
+        return options_gte
+    except configparser.NoSectionError:
+        return options_gte
+
+
+def load_gtc_configs(cfg_path: str = ""):
+    """Networkx Calculation Settings"""
+
+    options_gtc = {
+        "display_heatmaps": {"id": "display_heatmaps", "text": "Plot Heatmaps", "value": 1},
+        "display_degree_histogram": {"id": "display_degree_histogram", "text": "Average Degree", "value": 1},
+        "compute_network_diameter": {"id": "compute_network_diameter", "text": "Network Diameter", "value": 1},
+        "compute_graph_density": {"id": "compute_graph_density", "text": "Graph Density", "value": 1},
+        "compute_wiener_index": {"id": "compute_wiener_index", "text": "Wiener Index", "value": 1},
+        "compute_avg_node_connectivity": {"id": "compute_avg_node_connectivity", "text": "Average Node Connectivity", "value": 0},
+        "compute_global_efficiency": {"id": "compute_global_efficiency", "text": "Global Coefficient", "value": 1},
+        "compute_avg_clustering_coef": {"id": "compute_avg_clustering_coef", "text": "Average Clustering Coefficient", "value": 1},
+        "compute_assortativity_coef": {"id": "compute_assortativity_coef", "text": "Assortativity Coefficient", "value": 1},
+        "display_betweenness_centrality_histogram": {"id": "display_betweenness_centrality_histogram", "text": "Betweenness Centrality", "value": 1},
+        "display_closeness_centrality_histogram": {"id": "display_closeness_centrality_histogram", "text": "Closeness Centrality", "value": 1},
+        "display_eigenvector_centrality_histogram": {"id": "display_eigenvector_centrality_histogram", "text": "Eigenvector Centrality", "value": 1},
+        "display_edge_angle_centrality_histogram": {"id": "display_edge_angle_centrality_histogram", "text": "Edge Angle Centrality", "value": 0},
+        "display_ohms_histogram": {"id": "display_ohms_histogram", "text": "Ohms Centrality", "value": 0},
+        "compute_scaling_behavior": {"id": "compute_scaling_behavior", "text": "Scaling Behavior", "value": 0},
+        #"compute_lang": {"id": "compute_lang", "text": "Programming Language", "value": 'Py'}
+    }
+
+    # Load configuration from the file
+    config = read_config_file(cfg_path)
+    if config is None:
+        return options_gtc
+
+    try:
+        options_gtc["display_heatmaps"]["value"] = int(config.get('sgt-settings', 'display_heatmaps'))
+        options_gtc["display_degree_histogram"]["value"] = int(config.get('sgt-settings', 'display_degree_histogram'))
+        options_gtc["display_betweenness_centrality_histogram"]["value"] = int(config.get('sgt-settings', 'display_betweenness_centrality_histogram'))
+        options_gtc["display_closeness_centrality_histogram"]["value"] = int(config.get('sgt-settings', 'display_closeness_centrality_histogram'))
+        options_gtc["display_eigenvector_centrality_histogram"]["value"] = int(config.get('sgt-settings', 'display_eigenvector_centrality_histogram'))
+        options_gtc["compute_avg_node_connectivity"]["value"] = int(config.get('sgt-settings', 'compute_avg_node_connectivity'))
+        options_gtc["compute_graph_density"]["value"] = int(config.get('sgt-settings', 'compute_graph_density'))
+        options_gtc["compute_global_efficiency"]["value"] = int(config.get('sgt-settings', 'compute_global_efficiency'))
+        options_gtc["compute_avg_clustering_coef"]["value"] = int(config.get('sgt-settings', 'compute_avg_clustering_coef'))
+        options_gtc["compute_assortativity_coef"]["value"] = int(config.get('sgt-settings', 'compute_assortativity_coef'))
+        options_gtc["compute_network_diameter"]["value"] = int(config.get('sgt-settings', 'compute_network_diameter'))
+        options_gtc["compute_wiener_index"]["value"] = int(config.get('sgt-settings', 'compute_wiener_index'))
+        options_gtc["display_edge_angle_centrality_histogram"]["value"] = int(config.get('sgt-settings', 'display_edge_angle_centrality_histogram'))
+        options_gtc["display_ohms_histogram"]["value"] = int(config.get('sgt-settings', 'display_ohms_histogram'))
+        options_gtc["compute_scaling_behavior"]["value"] = int(config.get('sgt-settings', 'compute_scaling_behavior'))
+        # options_gtc["compute_lang"]["value"] = str(config.get('sgt-settings', 'compute_lang'))
+
+        return options_gtc
+    except configparser.NoSectionError:
+        return options_gtc

StructuralGT/utils/configs.ini

@@ -0,0 +1,97 @@
+[computation]
+cpu_cores = 0
+
+
+[image-dir]
+is_multi_image = 0
+image_path = ../datasets/np_images/mycelium_hyphae.png
+# Choose '../datasets/np_images/' for main_launcher or 'datasets/np_images/' for Terminal
+# Choose any of the image paths
+# image_path = ../datasets/np_images/InVitroBioFilm.png
+# image_path = ../datasets/np_images/tests/monkey.png
+# image_path = ../datasets/np_images/
+gt_output_path = ../results
+
+
+[filter-settings]
+# 0: global OR 1: adaptive OR 2: OTSU
+threshold_type = 0
+# range between 1-255
+global_threshold_value = 128
+# must be odd integer
+adaptive_local_threshold_value = 11
+# range between 0.01-5.0
+adjust_gamma = 1
+# must be odd integer
+blurring_window_size = 11
+filter_window_size = 1
+apply_gamma = 1
+apply_autolevel = 0
+apply_laplacian_gradient = 0
+apply_scharr_gradient = 0
+apply_sobel_gradient = 0
+apply_median_filter = 0
+apply_gaussian_blur = 0
+apply_lowpass_filter = 0
+apply_dark_foreground = 0
+# -100 to 100
+brightness_level = 0
+# -100 to 100
+contrast_level = 0
+scale_value_nanometers = 0
+scalebar_pixel_count = 1
+resistivity = 1
+save_images = 0
+
+
+
+[extraction-settings]
+merge_nearby_nodes = 1
+merge_node_radius_size = 3
+prune_dangling_edges = 1
+prune_max_iteration_count = 500
+remove_disconnected_segments = 1
+remove_self_loops = 1
+remove_object_size = 500
+display_node_id = 0
+add_weights = 0
+# DIA, AREA, LEN, ANGLE, INV_LEN, VAR_CON, FIX_CON, RES
+weight_type = DIA
+export_edge_list = 0
+export_as_gexf = 0
+export_adj_mat = 0
+export_as_gsd = 0
+
+
+[sgt-settings]
+display_heatmaps = 1
+display_degree_histogram = 1
+display_betweenness_centrality_histogram = 1
+display_closeness_centrality_histogram = 0
+display_eigenvector_centrality_histogram = 0
+display_edge_angle_centrality_histogram = 0
+display_ohms_histogram = 0
+compute_scaling_behavior = 0
+compute_avg_node_connectivity = 0
+compute_graph_density = 1
+compute_global_efficiency = 0
+compute_avg_clustering_coef = 1
+compute_assortativity_coef = 1
+compute_network_diameter = 1
+compute_wiener_index = 0
+compute_lang = Py
+
+
+[gnct-settings]
+ml_model = MLP
+
+
+[fic-settings]
+# reduce resolution (OPTIONAL)
+down_sampling_factor = 4
+domain_block_size = 8
+range_block_size = 4
+# should be 1 to get all candidates (overlapping)
+# having as 8 means no overlapping candidates (if domain_block_size=8)
+block_step_size = 8
+decompress_iteration_count = 25

StructuralGT/utils/progress_update.py

@@ -0,0 +1,67 @@
+# SPDX-License-Identifier: GNU GPL v3
+
+"""
+Uses listener functions to send updates to outside functions.
+"""
+
+
+class ProgressUpdate:
+    """
+    A class for sending updates to outside functions.
+
+    """
+    def __init__(self):
+        """
+        A class for sending updates to outside functions.
+
+        >>> def print_progress(code, msg):
+        >>>     print(str(code) + ': ' + str(msg))
+        >>>
+        >>> upd = ProgressUpdate()
+        >>> upd.add_listener(print_progress)  # to get updates
+        >>> upd.update_status([1,"Sending update ..."])
+        >>> upd.remove_listener(print_progress) # to opt out of updates
+        >>>
+        """
+        self.__listeners = []
+        self.abort = False
+
+    def abort_tasks(self):
+        """
+        Set abort flag.
+        :return:
+        """
+        self.abort = True
+
+    def add_listener(self, func):
+        """
+        Add functions from the list of listeners.
+        :param func:
+        :return:
+        """
+        if func in self.__listeners:
+            return
+        self.__listeners.append(func)
+
+    def remove_listener(self, func):
+        """
+        Remove functions from the list of listeners.
+        :param func:
+        :return:
+        """
+        if func not in self.__listeners:
+            return
+        self.__listeners.remove(func)
+
+    def update_status(self, args=None):
+        """
+        Run all the functions that are saved as listeners.
+
+        :param args:
+        :return:
+        """
+        # Trigger events.
+        if args is None:
+            args = []
+        for func in self.__listeners:
+            func(*args)