feat: Add JSON I/O functionality for surface points

.gitignore

@@ -1,5 +1,3 @@
-
-
 .vscode
 .idea
 .DS_Store
@@ -172,3 +170,14 @@ examples/integrations/*.out
 /.obsidian/core-plugins-migration.json
 /.obsidian/hotkeys.json
 /.obsidian/workspace.json
+
+# Ignore generated tutorial files
+examples/tutorials/z_other_tutorials/json_io/04_simple_layer_stack.py
+examples/tutorials/z_other_tutorials/json_io/fault_scalar_field.png
+examples/tutorials/z_other_tutorials/json_io/initial_model_y.png
+examples/tutorials/z_other_tutorials/json_io/model_with_data.png
+examples/tutorials/z_other_tutorials/json_io/multiple_series_faults_computed.json
+
+# Generated JSON files from examples
+examples/tutorials/z_other_tutorials/json_io/combination_model.json
+examples/tutorials/z_other_tutorials/json_io/combination_model_computed.json

examples/tutorials/z_other_tutorials/json_io/01_surface_points_io.py

@@ -0,0 +1,95 @@
+"""
+Tutorial for JSON I/O operations in GemPy - Surface Points
+=======================================================
+
+This tutorial demonstrates how to save and load surface points data using JSON files in GemPy.
+"""
+
+import json
+import numpy as np
+import gempy as gp
+from gempy.modules.json_io import JsonIO
+
+# Create a sample surface points dataset
+# ------------------------------------
+
+# Create some sample surface points
+x = np.array([0, 1, 2, 3, 4])
+y = np.array([0, 1, 2, 3, 4])
+z = np.array([0, 1, 2, 3, 4])
+ids = np.array([0, 0, 1, 1, 2])  # Three different surfaces
+nugget = np.array([0.00002, 0.00002, 0.00002, 0.00002, 0.00002])
+
+# Create name to id mapping
+name_id_map = {f"surface_{id}": id for id in np.unique(ids)}
+
+# Create a SurfacePointsTable
+surface_points = gp.data.SurfacePointsTable.from_arrays(
+    x=x,
+    y=y,
+    z=z,
+    names=[f"surface_{id}" for id in ids],
+    nugget=nugget,
+    name_id_map=name_id_map
+)
+
+# Create a JSON file with the surface points data
+# ---------------------------------------------
+
+# Create the JSON structure
+json_data = {
+    "metadata": {
+        "name": "sample_model",
+        "creation_date": "2024-03-19",
+        "last_modification_date": "2024-03-19",
+        "owner": "tutorial"
+    },
+    "surface_points": [
+        {
+            "x": float(x[i]),
+            "y": float(y[i]),
+            "z": float(z[i]),
+            "id": int(ids[i]),
+            "nugget": float(nugget[i])
+        }
+        for i in range(len(x))
+    ],
+    "orientations": [],
+    "faults": [],
+    "series": [],
+    "grid_settings": {
+        "regular_grid_resolution": [10, 10, 10],
+        "regular_grid_extent": [0, 4, 0, 4, 0, 4],
+        "octree_levels": None
+    },
+    "interpolation_options": {}
+}
+
+# Save the JSON file
+with open("sample_surface_points.json", "w") as f:
+    json.dump(json_data, f, indent=4)
+
+# Load the surface points from JSON
+# -------------------------------
+
+# Load the model from JSON
+loaded_surface_points = JsonIO._load_surface_points(json_data["surface_points"])
+
+# Verify the loaded data
+print("\nOriginal surface points:")
+print(surface_points)
+print("\nLoaded surface points:")
+print(loaded_surface_points)
+
+# Verify the data matches
+print("\nVerifying data matches:")
+print(f"X coordinates match: {np.allclose(surface_points.xyz[:, 0], loaded_surface_points.xyz[:, 0])}")
+print(f"Y coordinates match: {np.allclose(surface_points.xyz[:, 1], loaded_surface_points.xyz[:, 1])}")
+print(f"Z coordinates match: {np.allclose(surface_points.xyz[:, 2], loaded_surface_points.xyz[:, 2])}")
+print(f"IDs match: {np.array_equal(surface_points.ids, loaded_surface_points.ids)}")
+print(f"Nugget values match: {np.allclose(surface_points.nugget, loaded_surface_points.nugget)}")
+
+# Print the name_id_maps to compare
+print("\nName to ID mappings:")
+print(f"Original: {surface_points.name_id_map}")
+print(f"Loaded: {loaded_surface_points.name_id_map}") 

examples/tutorials/z_other_tutorials/json_io/02_horizontal_stratigraphic.py

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+"""
+Tutorial: Loading a Horizontal Stratigraphic Model using JSON I/O
+===============================================================
+
+This tutorial demonstrates how to load a horizontal stratigraphic model using GemPy's JSON I/O functionality.
+The model consists of two horizontal layers (rock1 and rock2) with surface points and orientations.
+"""
+
+# %%
+# Import necessary libraries
+import matplotlib
+matplotlib.use('Agg')  # Use non-interactive backend
+import gempy as gp
+import gempy_viewer as gpv
+import numpy as np
+import json
+from pathlib import Path
+import matplotlib.pyplot as plt
+from datetime import datetime
+
+# %%
+# Define the model data
+model_data = {
+    "metadata": {
+        "name": "Horizontal Stratigraphic Model",
+        "creation_date": "2024-03-24",
+        "last_modification_date": datetime.now().strftime("%Y-%m-%d"),
+        "owner": "GemPy Team"
+    },
+    "surface_points": [
+        {"x": 0.0, "y": 0.0, "z": 0.0, "id": 1, "nugget": 0.0},
+        {"x": 1.0, "y": 0.0, "z": 0.0, "id": 1, "nugget": 0.0},
+        {"x": 0.0, "y": 1.0, "z": 0.0, "id": 1, "nugget": 0.0},
+        {"x": 1.0, "y": 1.0, "z": 0.0, "id": 1, "nugget": 0.0},
+        {"x": 0.0, "y": 0.0, "z": 1.0, "id": 2, "nugget": 0.0},
+        {"x": 1.0, "y": 0.0, "z": 1.0, "id": 2, "nugget": 0.0},
+        {"x": 0.0, "y": 1.0, "z": 1.0, "id": 2, "nugget": 0.0},
+        {"x": 1.0, "y": 1.0, "z": 1.0, "id": 2, "nugget": 0.0}
+    ],
+    "orientations": [
+        {"x": 0.5, "y": 0.5, "z": 0.0, "G_x": 0.0, "G_y": 0.0, "G_z": 1.0, "id": 1, "nugget": 0.0, "polarity": 1},
+        {"x": 0.5, "y": 0.5, "z": 1.0, "G_x": 0.0, "G_y": 0.0, "G_z": 1.0, "id": 2, "nugget": 0.0, "polarity": 1}
+    ],
+    "series": [
+        {
+            "name": "series1",
+            "surfaces": ["layer1", "layer2"],
+            "structural_relation": "ERODE",
+            "colors": ["#ff0000", "#00ff00"]
+        }
+    ],
+    "grid_settings": {
+        "regular_grid_resolution": [10, 10, 10],
+        "regular_grid_extent": [0.0, 1.0, 0.0, 1.0, 0.0, 1.0],
+        "octree_levels": None
+    },
+    "interpolation_options": {
+        "kernel_options": {
+            "range": 1.7,
+            "c_o": 10
+        },
+        "mesh_extraction": True,
+        "number_octree_levels": 1
+    },
+    "fault_relations": None,
+    "id_name_mapping": {
+        "name_to_id": {
+            "layer1": 1,
+            "layer2": 2
+        }
+    }
+}
+
+# %%
+# Save the model data to a JSON file
+tutorial_dir = Path(__file__).parent
+json_file = tutorial_dir / "horizontal_stratigraphic.json"
+with open(json_file, "w") as f:
+    json.dump(model_data, f, indent=4)
+
+# %%
+# Load the model from JSON
+model = gp.modules.json_io.JsonIO.load_model_from_json(str(json_file))
+
+# %%
+# Compute the geological model
+gp.compute_model(model)
+
+# %%
+# Plot the model
+# Plot the initial geological model in the y direction without results
+fig, ax = plt.subplots(figsize=(10, 6))
+gpv.plot_2d(model, direction=['y'], show_results=False, ax=ax)
+plt.title("Initial Geological Model (y direction)")
+plt.savefig('initial_model_y.png')
+plt.close()
+
+# Plot the result of the model in the x and y direction with data and without boundaries
+fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(15, 6))
+gpv.plot_2d(model, direction=['x'], show_data=True, show_boundaries=False, ax=ax1)
+ax1.set_title("Model with Data (x direction)")
+gpv.plot_2d(model, direction=['y'], show_data=True, show_boundaries=False, ax=ax2)
+ax2.set_title("Model with Data (y direction)")
+plt.tight_layout()
+plt.savefig('model_with_data.png')
+plt.close()