Merge pull request #304 from cgre-aachen/dev_gemgis3

Dev gemgis3

.gitignore

@@ -100,6 +100,7 @@ share/python-wheels/
 *.egg-info/
 .installed.cfg
 *.egg
+.idea/*
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -239,3 +240,5 @@ examples/models/data/*
 examples/notebooks/data/*
 gemgis/__pycache__
 __pycache__
+
+_version_generated.py

MANIFEST.in

@@ -3,4 +3,6 @@ include README.md
 include requirements.txt
 include requirements_dev.txt
 
-recursive-exclude * __pycache__
+recursive-exclude * __pycache__
+
+exclude .git/* .idea/*

docs/conf.py

@@ -16,9 +16,7 @@
 copyright = "2020–2023, GemGIS Developers"
 author = 'Alexander Juestel'
 
-# The full version, including alpha/beta/rc tags
-release = '1.1.1'
-version = release
+
 
 # -- GemGIS configuration ---------------------------------------------------
 import os
@@ -29,6 +27,12 @@
 sys.path.insert(0, os.path.abspath("../gemgis/"))
 sys.path.insert(0, os.path.abspath("../../gemgis/"))
 
+# The full version, including alpha/beta/rc tags
+
+import gemgis as gg
+
+version = gg.__version__
+
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be

docs/getting_started/tutorial/65_displaying_seismic_horizons_and_faults.ipynb

@@ -2211,6 +2211,7 @@
   }
  ],
  "metadata": {
+  "hide_input": false,
   "kernelspec": {
    "display_name": "Python 3 (ipykernel)",
    "language": "python",
@@ -2226,7 +2227,36 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "version": "3.8.5"
+  },
+  "varInspector": {
+   "cols": {
+    "lenName": 16,
+    "lenType": 16,
+    "lenVar": 40
+   },
+   "kernels_config": {
+    "python": {
+     "delete_cmd_postfix": "",
+     "delete_cmd_prefix": "del ",
+     "library": "var_list.py",
+     "varRefreshCmd": "print(var_dic_list())"
+    },
+    "r": {
+     "delete_cmd_postfix": ") ",
+     "delete_cmd_prefix": "rm(",
+     "library": "var_list.r",
+     "varRefreshCmd": "cat(var_dic_list()) "
+    }
+   },
+   "types_to_exclude": [
+    "module",
+    "function",
+    "builtin_function_or_method",
+    "instance",
+    "_Feature"
+   ],
+   "window_display": false
   }
  },
  "nbformat": 4,

docs/getting_started/tutorial/71_Opening_Rasters_From_OpenFileGDB.ipynb

@@ -7,7 +7,9 @@
    "source": [
     "# 71 Opening Rasters from OpenFileGDB\n",
     "\n",
-    "This notebook illustrates how to open rasters that are stored in OpenFileGDBs. Currently, QGIS can open rasters from OpenFileGDBs since version 3.32. GeoPandas and the underlying fiona package are capable of opening vector files from OpenFileGDBs. It is not planned to support raster files (https://github.com/geopandas/geopandas/issues/2793). It is not planned to implement that feature into rasterio either (https://github.com/rasterio/rasterio/discussions/2914). Therefore, the decision was made to implement the functionality to open rasters from OpenFileGDBs directly using the `gdal` package. "
+    "This notebook illustrates how to open rasters that are stored in OpenFileGDBs. Currently, QGIS can open rasters from OpenFileGDBs since version 3.32. GeoPandas and the underlying fiona package are capable of opening vector files from OpenFileGDBs. It is not planned to support raster files (https://github.com/geopandas/geopandas/issues/2793). It is not planned to implement that feature into rasterio either (https://github.com/rasterio/rasterio/discussions/2914). Therefore, the decision was made to implement the functionality to open rasters from OpenFileGDBs directly using the `gdal` package. \n",
+    "\n",
+    "<img src=\"../images/tutorial71_cover.png\">"
    ]
   },
   {

environment_dev.yml

@@ -43,3 +43,4 @@ dependencies:
     - sphinx_automodapi
     - sphinx_numfig
     - numpydoc
+    - build

gemgis/__init__.py

@@ -20,8 +20,6 @@
 
 __version_date__ = '2023-09-23'
 
-__version__ = '1.1.1'
-
 __changelog__ = """What is new in version 1.1.0:
 
 

gemgis/download_gemgis_data.py

@@ -35,13 +35,17 @@ def create_pooch(storage_url: str,
             Base URL for the remote data source.
         files : List[str]
             A record of the files that are managed by this Pooch.
-        target : str, default: ''
+        target : str, default: ``''``
             The path to the local data storage folder, e.g. ``target='Documents/gemgis/'``.
 
     Returns
     _______
         pooch.core.Pooch
             Pooch class.
+
+    See also
+    ________
+        download_tutorial_data: Download the GemGIS data for each tutorial.
     """
     try:
         import pooch
@@ -67,11 +71,15 @@ def download_tutorial_data(filename: str,
     __________
         filename : str
             File name to be downloaded by pooch, e.g. ``filename='file.zip'``.
-        dirpath : str, default: ''
+        dirpath : str, default: ``''``
             Path to the directory where the data is being stored, default to the directory where the notebook is
             located, e.g. ``dirpath='Documents/gemgis/'``.
         storage_url : str, default 'https://rwth-aachen.sciebo.de/s/AfXRsZywYDbUF34/download?path=%2F'
             URL to the GemGIS data storage, default is the RWTH Aachen University Sciebo Cloud Storage.
+
+    See also
+    ________
+        create_pooch : Create pooch class to fetch files from a website.
     """
     try:
         import pooch

gemgis/misc.py

@@ -1,5 +1,5 @@
 """
-Contributors: Alexander Jüstel, Arthur Endlein Correia, Florian Wellmann, Marius Pischke
+Contributors: Alexander Jüstel, Arthur Endlein Correia, Florian Wellmann, Marius Pischke.
 
 GemGIS is a Python-based, open-source spatial data processing library.
 It is capable of preprocessing spatial data such as vector data
@@ -33,23 +33,21 @@
 
 def load_pdf(path: str,
              save_as_txt: bool = True) -> str:
-    """Function to load pdf containing borehole data
+    """
+    Load PDF file containing borehole data.
 
     Parameters
     __________
-
         path : str
-            Name of the PDF file, e.g. ``path='file.pdf'``
-
-        save_as_txt : bool
+            Name of the PDF file, e.g. ``path='file.pdf'``.
+        save_as_txt : bool, default: ``True``
             Variable to save the extracted data as txt file.
-            Options include: ``True`` or ``False``, default set to ``True``
+            Options include: ``True`` or ``False``.
 
     Returns
     _______
-
-        page_content : str
-            Extracted page content from borehole data
+        str
+            Extracted page content from borehole data.
 
     .. versionadded:: 1.0.x
 
@@ -66,14 +64,11 @@ def load_pdf(path: str,
 
     See Also
     ________
-
-        get_meta_data : Getting the meta data of a well
-        get_meta_data_df : Getting the meta data of wells as DataFrame
-        get_stratigraphic_data : Getting the stratigraphic data of a well
-        get_stratigraphic_data_df : Getting the stratigraphic data of wells as DataFrame
-
+        get_meta_data : Get the meta data of a well.
+        get_meta_data_df : Get the meta data of wells as DataFrame.
+        get_stratigraphic_data : Get the stratigraphic data of a well.
+        get_stratigraphic_data_df : Get the stratigraphic data of wells as DataFrame.
     """
-
     # Trying to import PyPDF2 but returning error if tqdm is not installed
     try:
         import PyPDF2

gemgis/raster.py

@@ -2716,7 +2716,8 @@ def extract_contour_lines_from_raster(raster: Union[rasterio.io.DatasetReader, n
 def read_raster_gdb(path: str,
                     crs: Union[str,
                                pyproj.crs.crs.CRS,
-                               rasterio.crs.CRS] = None):
+                               rasterio.crs.CRS] = None,
+                    path_out: str = ''):
     """Read Raster from OpenFileGDB.
 
     Parameters
@@ -2725,6 +2726,8 @@ def read_raster_gdb(path: str,
             Path to the OpenFileGDB.
         crs : str, pyproj.crs.crs.CRS, rasterio.crs.CRS
             Coordinate Reference System of the dataset.
+        path_out : str
+            Output folder path
 
     .. versionadded:: 1.1.1
 
@@ -2739,6 +2742,10 @@ def read_raster_gdb(path: str,
     if not isinstance(path, str):
         raise TypeError('Path to the OpenFileGDB must be provided as string')
 
+    # Checking that the output path is of type string
+    if not isinstance(path_out, str):
+        raise TypeError('Output path must be provided as string')
+
     # Opening Database
     ds = gdal.Open(path)
 
@@ -2768,7 +2775,7 @@ def read_raster_gdb(path: str,
 
         # Saving raster to file
         with rasterio.open(
-                ds.GetSubDatasets()[i][1].replace(' ', '') + '.tif',
+                path_out + ds.GetSubDatasets()[i][1].replace(' ', '') + '.tif',
                 'w',
                 driver='GTiff',
                 height=raster.shape[0],

gemgis/vector.py

@@ -623,7 +623,7 @@ def extract_xy(gdf: gpd.geodataframe.GeoDataFrame,
 
     .. versionchanged:: 1.1
        If a GeoDataFrame contains LineStrings and MultiLineStrings, the index of the exploded GeoDataFrame will now
-       be reset. Not resetting the index will cause index errors later on. 
+       be reset. Not resetting the index will cause index errors later on.
 
     Example
     _______

gemgis/visualization.py

@@ -797,7 +797,7 @@ def convert_to_rgb(array: np.ndarray) -> np.ndarray:
 def drape_array_over_dem(array: np.ndarray,
                          dem: Union[rasterio.io.DatasetReader, np.ndarray],
                          extent: List[Union[float, int]] = None,
-                         zmax: Union[float, int] = 1000,
+                         zmax: Union[float, int] = 10000,
                          resize_array: bool =True):
     """Creating grid and texture to drape array over a digital elevation model
 
@@ -834,6 +834,10 @@ def drape_array_over_dem(array: np.ndarray,
     .. versionchanged:: 1.1
        Function now allows rasters with different sizes and resizes one of the rasters automatically
 
+    .. versionchanged:: 1.1.2
+       Edit zmax value and fixing a bug with the scikit-image resize function,
+       see https://github.com/cgre-aachen/gemgis/issues/303
+
     Example
     _______
 
@@ -921,10 +925,12 @@ def drape_array_over_dem(array: np.ndarray,
 
         if resize_array:
             array = resize(image=array,
+                           preserve_range=True,
                            output_shape=(dem.shape[0],
                                          dem.shape[1]))
         else:
             dem = resize(image=dem,
+                         preserve_range=True,
                          output_shape=(array.shape[0],
                                        array.shape[1]))
 

pyproject.toml

@@ -3,6 +3,9 @@ requires = ["setuptools>=68.1.2",
             "setuptools_scm[toml]>=6.2"]
 build-backend = "setuptools.build_meta"
 
+[tool.setuptools]
+package-dir = { "" = "gemgis" }
+
 [project]
 name = "GemGIS"
 
@@ -17,8 +20,8 @@ description = "Spatial data processing for geomodeling"
 keywords = ["dataprocessing", "modeling", "geospatial", "geographic-data", "spatial-data", "rasterdata", "vectordata",
             "geographic", "geomodeling"]
 readme = "README.md"
-license = {file = LICENSE}
-dynamic = ["Version"]
+license = {file = "LICENSE"}
+dynamic = ['version']
 requires-python = ">=3.8"
 classifiers = [
     'Development Status :: 5 - Production/Stable',
@@ -32,9 +35,9 @@ classifiers = [
     'Operating System :: OS Independent',
 ]
 dependencies = [
-    geopandas,
-    rasterio,
-    pyvista,
+    'geopandas',
+    'rasterio',
+    'pyvista',
 ]
 [project.urls]
 Documentation = 'https://gemgis.readthedocs.io/'