Merge pull request #299 from cgre-aachen/dev_gemgis3

GemGIS 1.1.1

.github/workflows/pypi_release.yml

@@ -22,6 +22,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install setuptools wheel twine
+        pip install -r requirements.txt
     - name: Build and publish
       env:
         TWINE_USERNAME: ${{ secrets.PYPI_USERS }}

README.md

@@ -38,8 +38,8 @@ Furthermore, many [example models](https://gemgis.readthedocs.io/en/latest/getti
 <a name="installation"></a>
 ## Installation
 It is recommended to use GemGIS with **python">=3.10"** in a separated environment. The main packages and its dependencies can be installed via the conda-forge channel. GemGIS is then available through PyPi or Conda. 
-1) `conda install -c conda-forge geopandas">=0.12.2" rasterio">=1.3.4"`
-2) `conda install -c conda-forge pyvista">=0.37.0"`
+1) `conda install -c conda-forge geopandas">=0.13.2" rasterio">=1.3.8"`
+2) `conda install -c conda-forge pyvista">=0.42.1"`
 3) `pip install gemgis` / `conda install -c conda-forge gemgis`
 
 Check out the [Installation Page](https://gemgis.readthedocs.io/en/latest/getting_started/installation.html) for more detailed instructions. 

docs/conf.py

@@ -17,7 +17,7 @@
 author = 'Alexander Juestel'
 
 # The full version, including alpha/beta/rc tags
-release = '1.1.0'
+release = '1.1.1'
 version = release
 
 # -- GemGIS configuration ---------------------------------------------------

docs/getting_started/installation.rst

@@ -1,6 +1,6 @@
 .. _installation_ref:
 
-Installation (Tested 2023-01-01)
+Installation (Tested 2023-09-01)
 ===========================================================
 
 GemGIS is supported on Python version 3.10. Previous versions are officially not supported.
@@ -96,15 +96,15 @@ Installing GemGIS's dependencies manually
 
 Two of the main packages that GemGIS is dependent on are `rasterio <https://rasterio.readthedocs.io/en/latest/>`_ and `GeoPandas <https://geopandas.org/>`_. It is recommended to install these packages separately as they both depend on the `GDAL <https://gdal.org/>`_ translator library for raster and vector geospatial data. In addition, many smaller libraries like shaply or fiona will also be installed properly.
 
-Install the latest versions of GeoPandas and Rasterio (as of 2023-01-01). Please mind the quotation marks that are necessary when specifying the version numbers.::
+Install the latest versions of GeoPandas and Rasterio (as of 2023-09-01). Please mind the quotation marks that are necessary when specifying the version numbers.::
 
-   conda install -c conda-forge geopandas">=0.12.2" rasterio">=1.3.4"
+   conda install -c conda-forge geopandas">=0.13.2" rasterio">=1.3.8"
 
 .. image:: images/cmd6.png
 
 In order to visualize and work with meshes, the `PyVista <https://docs.pyvista.org/>`_ package is being installed::
 
-    conda install -c conda-forge pyvista">=0.37.0"
+    conda install -c conda-forge pyvista">=0.42."
 
 
 Installing GemGIS via PyPi

docs/getting_started/tutorial/index.rst

@@ -106,4 +106,6 @@ Each set of functions of GemGIS is collected in a different module. The function
     65_displaying_seismic_horizons_and_faults
     66_generating_voronoi_polygons
     67_rotating_gempy_input_data
-    68_Creating_Finite_Faults_with_GemGIS
+    68_Creating_Finite_Faults_with_GemGIS
+    70_Reprojecting_Seismic_Data
+    71_Opening_Rasters_From_OpenFileGDB

gemgis/__init__.py

@@ -18,15 +18,19 @@
 
 __affiliations__ = 'CGRE - RWTH Aachen University'
 
-__version_date__ = '2023-08-18'
+__version_date__ = '2023-09-23'
 
-__version__ = '1.1.0'
+__version__ = '1.1.1'
 
 __changelog__ = """What is new in version 1.1.0:
 
 
 
 """
+try:
+    from ._version_generated import __version__
+except ImportError:
+    __version__ = "unreleased"
 
 from gemgis.gemgis import *
 import gemgis.vector as vector

gemgis/postprocessing.py

@@ -1074,21 +1074,11 @@ def clip_fault_of_gempy_model(geo_model,
             raise ValueError('Fault is not part of the GemPy geo_model')
 
         # Getting the fault DataFrames
-        fault_df_interfaces = gp.get_data(geo_model, 'surface_points')[
-            gp.get_data(geo_model,
-                        'surface_points')['surface'] == fault].reset_index(drop=True)
+        fault_df_interfaces = geo_model.surface_points.df[
+            geo_model.surface_points.df['surface'] == fault].reset_index(drop=True)
 
-        fault_df_orientations1 = gp.get_data(geo_model,
-                                             'orientations',
-                                             numeric=False)
-        fault_df_orientations2 = gp.get_data(geo_model,
-                                             'orientations',
-                                             numeric=True)
-
-        fault_df_orientations = fault_df_orientations1.merge(fault_df_orientations2,
-                                                             how='inner')
-
-        fault_df_orientations = fault_df_orientations[fault_df_orientations['surface'] == fault].reset_index(drop=True)
+        fault_df_orientations = geo_model.orientations.df[
+            geo_model.orientations.df['surface'] == fault].reset_index(drop=True)
 
     # Checking that the parameter which is of type string or list of strings
     if not isinstance(which, str):

gemgis/raster.py

@@ -2711,3 +2711,74 @@ def extract_contour_lines_from_raster(raster: Union[rasterio.io.DatasetReader, n
     gdf_lines['Z'] = values
 
     return gdf_lines
+
+
+def read_raster_gdb(path: str,
+                    crs: Union[str,
+                               pyproj.crs.crs.CRS,
+                               rasterio.crs.CRS] = None):
+    """Read Raster from OpenFileGDB.
+
+    Parameters
+    __________
+        path : str
+            Path to the OpenFileGDB.
+        crs : str, pyproj.crs.crs.CRS, rasterio.crs.CRS
+            Coordinate Reference System of the dataset.
+
+    .. versionadded:: 1.1.1
+
+    """
+    # Trying to import osgeo but returning error if tqdm is not installed
+    try:
+        from osgeo import gdal, osr
+    except ModuleNotFoundError:
+        raise ModuleNotFoundError('osgeo package is not installed')
+
+    # Checking that the path is of type string
+    if not isinstance(path, str):
+        raise TypeError('Path to the OpenFileGDB must be provided as string')
+
+    # Opening Database
+    ds = gdal.Open(path)
+
+    # Getting the length of the subsets
+    len_subdatasets = len(ds.GetSubDatasets())
+
+    # Performing workflow for every dataset
+    for i in range(len_subdatasets):
+        # Getting the name of the layer
+        layer = ds.GetSubDatasets()[i][0]
+        # Opening the raster layer
+        dataset = gdal.Open(layer)
+        # Getting the first raster band
+        raster_band = dataset.GetRasterBand(1)
+        # Getting raster values as array
+        raster = raster_band.ReadAsArray()
+
+        # Creating CRS from projection or manually
+        if dataset.GetProjection():
+            proj = osr.SpatialReference(wkt=dataset.GetProjection())
+            epsg = proj.GetAttrValue('AUTHORITY', 1)
+            crs = 'EPSG:' + epsg
+        else:
+            if not crs:
+                raise ValueError(
+                    'Raster does not have a projection, please provide a valid coordinate reference system')
+
+        # Saving raster to file
+        with rasterio.open(
+                ds.GetSubDatasets()[i][1].replace(' ', '') + '.tif',
+                'w',
+                driver='GTiff',
+                height=raster.shape[0],
+                width=raster.shape[1],
+                count=1,
+                dtype=raster.dtype,
+                crs=crs,
+                transform=affine.Affine.from_gdal(*dataset.GetGeoTransform()),
+                nodata=raster_band.GetNoDataValue()
+        ) as dst:
+            dst.write(raster, 1)
+
+        print(ds.GetSubDatasets()[i][1].replace(' ', '') + '.tif successfully saved to file')