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/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/71_Opening_Rasters_From_OpenFileGDB.ipynb

@@ -0,0 +1,113 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "86f44ca3",
+   "metadata": {},
+   "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. "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "e7147456",
+   "metadata": {},
+   "source": [
+    "## Set File Paths and download Tutorial Data\n",
+    "\n",
+    "If you downloaded the latest `GemGIS` version from the Github repository, append the path so that the package can be imported successfully. Otherwise, it is recommended to install `GemGIS` via `pip install gemgis` and import `GemGIS` using `import gemgis as gg`. In addition, the file path to the folder where the data is being stored is set. The tutorial data is downloaded using Pooch (https://www.fatiando.org/pooch/latest/index.html) and stored in the specified folder. Use `pip install pooch` if Pooch is not installed on your system yet."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "eb8af06a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import warnings\n",
+    "warnings.filterwarnings(\"ignore\")\n",
+    "\n",
+    "import gemgis as gg"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "a4128de8",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "file_path ='data/71_Opening_Rasters_From_OpenFileGDB/'"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "fb73e2b2-98ab-472d-bb33-e12d82240790",
+   "metadata": {},
+   "source": [
+    "## Opening OpenFileGDB\n",
+    "\n",
+    "The OpenFileGDB can be opened using the GemGIS function `gg.raster.read_raster_gdb(...)`. It will automatically save all included rasters to file. If there is no projection included in the OpenFileGDB, a `crs` must be provided manually."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "fdbd8040-ba16-4047-881d-59358d2289c8",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "RasterCenoman_Turon_top.tif successfully saved to file\n",
+      "RasterCenoman_Turon_m.tif successfully saved to file\n",
+      "RasterDevon_MK_m.tif successfully saved to file\n",
+      "RasterDevon_MK_top.tif successfully saved to file\n",
+      "RasterUKarb_m.tif successfully saved to file\n",
+      "RasterUKarb_top.tif successfully saved to file\n",
+      "RasterDGM.tif successfully saved to file\n"
+     ]
+    }
+   ],
+   "source": [
+    "gg.raster.read_raster_gdb(file_path + 'OpenFileGDB.gdb', \n",
+    "                          crs='EPSG:25832')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1d9f4836-6af6-40e6-a882-c6f63d0321e0",
+   "metadata": {},
+   "source": [
+    "## Opening Rasters using Rasterio\n",
+    "\n",
+    "The downloaded rasters can be opened using the rasterio package as any other raster. "
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

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/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')