Last formal updates before new release

Author: geograz

README.md

@@ -17,7 +17,7 @@ The following publications have been produced as part of the Parametric Rock Mas
 
 
 ## Supplementary data
-Due to size limitations on Github, large data has to be moved to other repositories. Exemplary sample data from PDD1 sample with ID 151763271961 can be found in the folder 'sample_data'. Two external datasets are currently connected to the repository:
+Due to size limitations on Github, large data has to be moved to other repositories. Exemplary sample data from PDD1 sample with ID 151763271961 can be found in the folder `sample_data`. Two external datasets are currently connected to the repository:
 
 - The original **Parametric Discontinuity Dataset 1 (PDD1)**: the dataset was created as part of Erharter (2024). It consists of 5000 meshes that comprise synthetic rock mass models in the form of 10 x 10 x 10 m cubes with discontinuities. It can be found on *Zenodo* under this link: https://doi.org/10.5281/zenodo.15835130
 - The **raster models of PDD1** that were created as part of Erharter and Elmo (2025). All 5000 models of PDD1 were rastered at resolutions of 0.25, 0.2, 0.15, 0.1 and 0.05 m. Total = 25 000 rasters. The dataset can be found on *Zenodo* under this link: https://doi.org/10.5281/zenodo.15570244

src/A_compiler.py

@@ -7,13 +7,24 @@
 
 Script that compiles the recorded data from samples of the discrete
 discontinuity networks and creates one excel file for further processing.
+
+NOTE: this script goes back to the creation of the original PDD1. It was
+necessary to compile a single dataset of the mesh models and further metadata
+that was saved in Grasshopper. The mesh files are now all in Zenodo
+repositories and the Grasshopper Metadata in a zipped folder in this repo. This
+script consequently won't work in the current form.
+In future versions it will be removed.
+-> IF YOU WANT TO COMPILE PDD1 FROM SCRATCH, IT IS BEST TO DO THIS FROM THE
+2023 RELEASE OF THE REPOSITORY
+https://github.com/geograz/Parametric_Rockmass_Studies/releases/tag/v1.0.0
 """
 
+from os import listdir
+import pickle
+
 import gzip
 import numpy as np
-from os import listdir
 import pandas as pd
-import pickle
 from tqdm import tqdm
 
 

src/B_analyzer.py

@@ -9,10 +9,11 @@
 dataset, computes new parameters and creates figures to visualize the dataset.
 """
 
+import pickle
+
 import gzip
 import numpy as np
 import pandas as pd
-import pickle
 from skimage.measure import euler_number
 from tqdm import tqdm
 

src/C_rasterizer.py

@@ -9,13 +9,14 @@
 for further analyses. Does not include raster analyses - only generation.
 """
 
+from os import listdir
+
 import gzip
 import pickle
 import gc
 import numpy as np
 import pandas as pd
 import trimesh
-from os import listdir
 
 from X_library import parameters, utilities
 

src/D_Voxel_export.py

@@ -8,21 +8,20 @@
 Script that saves a mesh of a rastered sample. For visualization purposes only.
 """
 
-import os
-
 import trimesh
+from X_library import utilities
+
+utils = utilities()
 
 SAMPLE = 151763271961  # sample with ID to process
 RESOLUTIONS = [0.25, 0.2, 0.15, 0.1, 0.05]  # 3D voxel resolution
 
-# get the directory where the current python file is
-script_dir = os.path.dirname(os.path.abspath(__file__))
-
-
 for resolution in RESOLUTIONS:
-    fp = os.path.abspath(os.path.join(script_dir, '..', fr'sample_data\{SAMPLE}_discontinuities.stl'))
+    fp = utils.make_rel_fp(
+        fr'sample_data\{SAMPLE}_discontinuities.stl', 1)
     discontinuity_mesh = trimesh.load_mesh(fp)
     discontinuity_voxels = discontinuity_mesh.voxelized(pitch=resolution)
     voxel_mesh = discontinuity_voxels.as_boxes()
-    fp = os.path.abspath(os.path.join(script_dir, '..', fr'sample_data\{SAMPLE}_{resolution}_voxel_mesh.stl'))
+    fp = utils.make_rel_fp(
+        fr'sample_data\{SAMPLE}_{resolution}_voxel_mesh.stl', 1)
     voxel_mesh.export(fp)

src/F_MeshChecker.py

@@ -8,9 +8,10 @@
 Script that performs different checks of the generated meshes.
 """
 
-import trimesh
 from os import listdir
 
+import trimesh
+
 # get ids of all generated meshes
 ids = [c.split('_')[0] for c in listdir(r'../combinations') if 'discontinuities' in c]
 

src/X_library.py

@@ -9,6 +9,9 @@
 math, general use (utilities), plotting and computation of parameters.
 """
 
+import os
+import zlib
+
 import numpy as np
 import pandas as pd
 from scipy.ndimage import generic_filter, label
@@ -21,13 +24,13 @@
 import trimesh
 import matplotlib
 import matplotlib.gridspec as gridspec
-import zlib
 matplotlib.use('Agg')
 import matplotlib.pyplot as plt
 from matplotlib.ticker import FormatStrFormatter
 
 
 class math:
+    '''class with mathematical functions'''
 
     def __init__(self):
         pass
@@ -54,6 +57,7 @@ def normal_vectors(self, dips, dipdirs):
 
 
 class utilities:
+    '''class with miscaleneous functions that don't fit anywhere else'''
 
     def __init__(self):
         self.sclr = MinMaxScaler()
@@ -140,8 +144,22 @@ def identify_intact_rock_regions(self, array: np.array) -> list:
 
         return labeled_array, num_features
 
+    def make_rel_fp(self, path: str, levels_up: int = 0) -> str:
+        '''function creates a relative filepath from the executing python file
+        location'''
+        script_dir = os.path.dirname(os.path.abspath(__file__))
+        if levels_up > 0:
+            lvls = ['..'] * levels_up
+            path_list = [script_dir] + lvls + [path]
+        else:
+            path_list = [script_dir, path]
+        return os.path.abspath(os.path.join(*path_list))
+
+
+
 
 class plotter(utilities):
+    '''class with plotting functions'''
 
     def __init__(self):
         self.label_map = {
@@ -718,6 +736,8 @@ def Euler_plot(self) -> None:
 
 
 class parameters:
+    '''class with functions that compute rock engineering parameters of rock
+    mass structures'''
 
     def __init__(self):
         pass