las-geoh5 0.1.0__tar.gz

las_geoh5-0.1.0/LICENSE.txt

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+MIT License
+
+Copyright (c) 2023 Mira Geoscience
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

las_geoh5-0.1.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: las-geoh5
+Version: 0.1.0
+Summary: Las/Geoh5 conversion
+Home-page: https://mirageoscience.com
+License: MIT
+Keywords: geology,geophysics,earth sciences,io,data,interoperability
+Author: Mira Geoscience
+Author-email: support@mirageoscience.com
+Requires-Python: >=3.9,<3.11
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Natural Language :: English
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: POSIX
+Classifier: Operating System :: Unix
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Dist: geoh5py (>=0.8.0rc3,<0.9.0)
+Requires-Dist: lasio (>=0.31,<0.32)
+Requires-Dist: tqdm (>=4.64.0,<5.0.0)
+Description-Content-Type: text/x-rst
+
+las-geoh5
+=========
+
+Import/Export LAS files to/from geoh5 format.
+
+This package contains three modules for import/export of LAS files in
+and out of a geoh5 file. the import/export directories modules allow
+export and subsequent re-import of LAS files from a drillhole group
+saved in a geoh5 file to a structured set of directories on disk. The
+import files module is intended for the more general case of LAS file
+import to an existing drillhole group.
+
+Basic Usage
+-----------
+.. _Geoscience ANALYST Pro: https://mirageoscience.com/mining-industry-software/geoscience-analyst-pro/
+
+The most convenient way to use this package is through `Geoscience ANALYST Pro`_
+where the import files driver may be run from the **file -> import**
+menu.
+
+All drivers may also be run from a ui.json file in `Geoscience ANALYST Pro`_
+by either adding to the Python Scripts directory or drag and drop into
+the viewport. Defaulted ui.json files can be found in the uijson folder
+of the las-geoh5 project.
+
+Finally, the drivers can be run from CLI using the following
+
+.. code:: bash
+
+   python -m las_geoh5.module.driver some_file.ui.json
+
+Where module is one of ``import_files``, ``export_files``, or ``import_las``.
+
+License
+-------
+
+MIT License
+
+Copyright (c) 2023 Mira Geoscience
+
+Permission is hereby granted, free of charge, to any person obtaining a
+copy of this software and associated documentation files (the
+“Software”), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be included
+in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS
+OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+

las_geoh5-0.1.0/README.rst

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+las-geoh5
+=========
+
+Import/Export LAS files to/from geoh5 format.
+
+This package contains three modules for import/export of LAS files in
+and out of a geoh5 file. the import/export directories modules allow
+export and subsequent re-import of LAS files from a drillhole group
+saved in a geoh5 file to a structured set of directories on disk. The
+import files module is intended for the more general case of LAS file
+import to an existing drillhole group.
+
+Basic Usage
+-----------
+.. _Geoscience ANALYST Pro: https://mirageoscience.com/mining-industry-software/geoscience-analyst-pro/
+
+The most convenient way to use this package is through `Geoscience ANALYST Pro`_
+where the import files driver may be run from the **file -> import**
+menu.
+
+All drivers may also be run from a ui.json file in `Geoscience ANALYST Pro`_
+by either adding to the Python Scripts directory or drag and drop into
+the viewport. Defaulted ui.json files can be found in the uijson folder
+of the las-geoh5 project.
+
+Finally, the drivers can be run from CLI using the following
+
+.. code:: bash
+
+   python -m las_geoh5.module.driver some_file.ui.json
+
+Where module is one of ``import_files``, ``export_files``, or ``import_las``.
+
+License
+-------
+
+MIT License
+
+Copyright (c) 2023 Mira Geoscience
+
+Permission is hereby granted, free of charge, to any person obtaining a
+copy of this software and associated documentation files (the
+“Software”), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be included
+in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS
+OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

las_geoh5-0.1.0/las_geoh5/__init__.py

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+#  Copyright (c) 2023 Mira Geoscience Ltd.
+#
+#  This file is part of las_geoh5 project.
+#
+#  las-geoh5 is distributed under the terms and conditions of the MIT License
+#  (see LICENSE file at the root of this source code package).
+#
+
+# flake8: noqa
+
+__version__ = "0.1.0"

las_geoh5-0.1.0/las_geoh5/export_directories/__init__.py

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+#  Copyright (c) 2023 Mira Geoscience Ltd.
+#
+#  This file is part of las-geoh5 project.
+#
+#  las-geoh5 is distributed under the terms and conditions of the MIT License
+#  (see LICENSE file at the root of this source code package).
+#

las_geoh5-0.1.0/las_geoh5/export_directories/driver.py

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+#  Copyright (c) 2023 Mira Geoscience Ltd.
+#
+#  This file is part of las-geoh5 project.
+#
+#  las-geoh5 is distributed under the terms and conditions of the MIT License
+#  (see LICENSE file at the root of this source code package).
+#
+
+from __future__ import annotations
+
+import sys
+from pathlib import Path
+
+from geoh5py.groups import DrillholeGroup
+from geoh5py.objects import Drillhole
+from geoh5py.shared.utils import fetch_active_workspace
+from geoh5py.ui_json import InputFile
+from tqdm import tqdm
+
+from las_geoh5.export_las import drillhole_to_las
+
+
+def run(file: str | Path):
+    ifile = InputFile.read_ui_json(file)
+    dh_group = ifile.data["drillhole_group"]
+    name = ifile.data["name"]
+    with fetch_active_workspace(ifile.data["geoh5"]):
+        export_las_directory(dh_group, Path(ifile.path), name)
+
+
+def export_las_directory(
+    group: DrillholeGroup, basepath: str | Path, name: str | None = None
+):
+    """
+    Export contents of drillhole group to las files organized by directories.
+
+    :param group: Drillhole group container.
+    :param basepath: Base path where directories/files will be created.
+    :param name: Alternate name of root directory to be created.
+    """
+
+    if isinstance(basepath, str):
+        basepath = Path(basepath)
+
+    drillholes = [k for k in group.children if isinstance(k, Drillhole)]
+
+    name = name if name is not None else group.name
+    subpath = basepath / name
+    if not subpath.exists():
+        subpath.mkdir()
+
+    print(f"Exporting drillhole surveys and property group data to {str(subpath)}")
+    for drillhole in tqdm(drillholes):
+        drillhole_to_las(drillhole, subpath)
+
+
+if __name__ == "__main__":
+    run(sys.argv[1])

las_geoh5-0.1.0/las_geoh5/export_directories/uijson.py

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+#  Copyright (c) 2023 Mira Geoscience Ltd.
+#
+#  This file is part of las-geoh5 project.
+#
+#  las-geoh5 is distributed under the terms and conditions of the MIT License
+#  (see LICENSE file at the root of this source code package).
+#
+
+
+ui_json = {
+    "title": "Drillhole group to LAS file directories",
+    "geoh5": None,
+    "run_command": "las_geoh5.export_directories.driver",
+    "run_command_boolean": {
+        "value": False,
+        "label": "Run python module",
+        "main": True,
+        "tooltip": "Warning: launches process to run python model on save",
+    },
+    "monitoring_directory": None,
+    "conda_environment": "las-geoh5",
+    "conda_environment_boolean": False,
+    "workspace": None,
+    "drillhole_group": {
+        "main": True,
+        "label": "Drillhole group",
+        "value": None,
+        "groupType": ["{825424fb-c2c6-4fea-9f2b-6cd00023d393}"],
+    },
+    "name": {
+        "main": True,
+        "label": "Property group name",
+        "value": None,
+        "optional": True,
+        "enabled": False,
+    },
+}

las_geoh5-0.1.0/las_geoh5/export_las.py

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+#  Copyright (c) 2023 Mira Geoscience Ltd.
+#
+#  This file is part of las-geoh5 project.
+#
+#  las-geoh5 is distributed under the terms and conditions of the MIT License
+#  (see LICENSE file at the root of this source code package).
+#
+
+from __future__ import annotations
+
+from pathlib import Path
+
+from geoh5py.data import ReferencedData
+from geoh5py.objects import Drillhole
+from geoh5py.shared.concatenation import ConcatenatedPropertyGroup
+from lasio import HeaderItem, LASFile
+
+
+def add_well_data(
+    file: LASFile,
+    drillhole: Drillhole,
+) -> LASFile:
+    """
+    Populate las file well data from drillhole.
+
+    :param file: lasio file object.
+    :param drillhole: geoh5py drillhole object.
+
+    :returns: Updated lasio file object.
+    """
+
+    # Add well name
+    file.well["WELL"] = drillhole.name
+
+    # Add epsg code
+    if drillhole.coordinate_reference_system is not None:
+        file.well.append(
+            HeaderItem(
+                mnemonic="GDAT",
+                value=drillhole.coordinate_reference_system["Code"],
+                descr=drillhole.coordinate_reference_system["Name"],
+            )
+        )
+
+    # Add collar data
+    file.well.append(HeaderItem(mnemonic="X", value=float(drillhole.collar["x"])))
+    file.well.append(HeaderItem(mnemonic="Y", value=float(drillhole.collar["y"])))
+    file.well.append(HeaderItem(mnemonic="ELEV", value=float(drillhole.collar["z"])))
+
+    return file
+
+
+def add_curve_data(file: LASFile, drillhole: Drillhole, group):
+    """
+    Populate las file with curve data from each property in group.
+
+    :param file: lasio file object.
+    :param drillhole: geoh5py.drillhole object containing property
+        groups for collocated data.
+    :param group: Property group containing collocated float data
+        objects of 'drillhole'.
+    """
+
+    if not isinstance(group, ConcatenatedPropertyGroup):
+        raise TypeError("Property group must be of type ConcatenatedPropertyGroup.")
+
+    if group.depth_:
+        file.append_curve("DEPTH", group.depth_.values, unit="m")
+    else:
+        file.append_curve("DEPTH", group.from_.values, unit="m", descr="FROM")
+        file.append_curve("TO", group.to_.values, unit="m", descr="TO")
+
+    properties = [] if group.properties is None else group.properties
+    data = [drillhole.get_data(k)[0] for k in properties]
+    filtered_data = [k for k in data if len(k.values) != 0]
+    for datum in filtered_data:
+        if any(k in datum.name for k in ["FROM", "TO", "DEPT"]):
+            continue
+
+        file.append_curve(datum.name, datum.values)
+
+        if isinstance(datum, ReferencedData):
+            for k, v in datum.value_map.map.items():  # pylint: disable=invalid-name
+                file.params.append(
+                    HeaderItem(
+                        mnemonic=f"{datum.name} ({k})", value=v, descr="REFERENCE"
+                    )
+                )
+
+    return file
+
+
+def add_survey_data(file: LASFile, drillhole: Drillhole) -> LASFile:
+    """
+    Add drillhole survey data to LASFile object.
+
+    :param file: las file object.
+    :param drillhole: drillhole containing survey data.
+
+    :return: Updated las file object.
+    """
+
+    # Add survey data
+    file.append_curve("DEPTH", drillhole.surveys[:, 0], unit="m")
+    file.append_curve(
+        "DIP",
+        drillhole.surveys[:, 1],
+        unit="degrees",
+        descr="from horizontal",
+    )
+    file.append_curve(
+        "AZIM",
+        drillhole.surveys[:, 2],
+        unit="degrees",
+        descr="from north (clockwise)",
+    )
+
+    return file
+
+
+def write_curves(
+    drillhole: Drillhole,
+    basepath: str | Path,
+    directory: bool = True,
+):
+    """
+    Write a formatted .las file for each property group in 'drillhole'.
+
+    :param drillhole: geoh5py drillhole object containing property
+        groups for collocated data.
+    :param basepath: Path to working directory.
+    :param directory: True if data is stored in sub-directories
+    """
+
+    if isinstance(basepath, str):
+        basepath = Path(basepath)
+
+    if not drillhole.property_groups:
+        raise AttributeError("Drillhole doesn't have any associated property groups.")
+
+    for group in drillhole.property_groups:
+        if group.property_group_type not in ["Interval table", "Depth table"]:
+            continue  # bypasses strike and dip groups
+
+        if group.name == "Static-Survey":
+            continue  # bypasses survey data handled elsewhere
+
+        file = LASFile()
+        file = add_well_data(file, drillhole)
+        file = add_curve_data(file, drillhole, group)
+
+        if not [
+            k for k in file.curves if k.mnemonic not in ["FROM", "TO", "DEPTH", "DEPT"]
+        ]:
+            continue
+
+        if directory:
+            subpath = basepath / group.name
+            if not subpath.exists():
+                subpath.mkdir()
+            filename = f"{drillhole.name}.las"
+        else:
+            subpath = basepath
+            filename = f"{drillhole.name}_{group.name}.las"
+
+        with open(
+            subpath / filename, "a", encoding="utf8"
+        ) as io:  # pylint: disable=invalid-name
+            file.write(io)
+
+
+def write_survey(
+    drillhole: Drillhole,
+    basepath: str | Path,
+    directory: bool = True,
+):
+    """
+    Write a formatted .las file with survey data from 'drillhole'.
+
+    :param drillhole: geoh5py drillhole object containing property
+        groups for collocated data.
+    :param basepath: Path to working directory.
+    :param directory: True if data is stored in sub-directories
+    """
+
+    if isinstance(basepath, str):
+        basepath = Path(basepath)
+
+    file = LASFile()
+    file = add_well_data(file, drillhole)
+    file = add_survey_data(file, drillhole)
+
+    if directory:
+        basepath = basepath / "Surveys"
+        if not basepath.exists():
+            basepath.mkdir()
+        filename = f"{drillhole.name}.las"
+    else:
+        filename = f"{drillhole.name}_survey.las"
+
+    with open(
+        basepath / filename, "a", encoding="utf8"
+    ) as io:  # pylint: disable=invalid-name
+        file.write(io)
+
+
+def drillhole_to_las(
+    drillhole: Drillhole,
+    basepath: str | Path,
+    directory: bool = True,
+):
+    """
+    Write a formatted .las file with data from 'drillhole'.
+
+    :param drillhole: geoh5py drillhole object containing property
+        groups for collocated data.
+    :param basepath: Path to working directory.
+    :param directory: True if data is stored in sub-directories
+    """
+
+    write_survey(drillhole, basepath, directory)
+    write_curves(drillhole, basepath, directory)

las_geoh5-0.1.0/las_geoh5/import_directories/__init__.py

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+#  Copyright (c) 2023 Mira Geoscience Ltd.
+#
+#  This file is part of las-geoh5 project.
+#
+#  las-geoh5 is distributed under the terms and conditions of the MIT License
+#  (see LICENSE file at the root of this source code package).
+#

las_geoh5-0.1.0/las_geoh5/import_directories/driver.py

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+#  Copyright (c) 2023 Mira Geoscience Ltd.
+#
+#  This file is part of las-geoh5 project.
+#
+#  las-geoh5 is distributed under the terms and conditions of the MIT License
+#  (see LICENSE file at the root of this source code package).
+#
+
+from __future__ import annotations
+
+import sys
+from pathlib import Path
+
+import lasio
+from geoh5py import Workspace
+from geoh5py.groups import DrillholeGroup
+from geoh5py.shared.utils import fetch_active_workspace
+from geoh5py.ui_json import InputFile
+
+from las_geoh5.import_las import las_to_drillhole
+
+
+def run(file: str):
+    ifile = InputFile.read_ui_json(file)
+    dh_group = ifile.data["drillhole_group"]
+    name = ifile.data["name"]
+    with fetch_active_workspace(ifile.data["geoh5"], mode="a") as workspace:
+        basepath = Path(ifile.path) / dh_group
+        import_las_directory(workspace, basepath, name)
+
+
+def import_las_directory(
+    workspace: Workspace, basepath: str | Path, name: str | None = None
+):
+    """
+    Import directory/files from previous export.
+
+    :param workspace: Project workspace.
+    :param basepath: Root directory for las data.
+    :param name: Alternate name for property group to create.
+
+    :return: New drillhole group containing imported items.
+    """
+
+    if isinstance(basepath, str):
+        basepath = Path(basepath)
+
+    if not basepath.exists():
+        raise OSError(f"Path {str(basepath)} does not exist.")
+
+    name = name if name is not None else basepath.name
+    dh_group = DrillholeGroup.create(workspace, name=name)
+
+    surveys_path = basepath / "Surveys"
+    surveys = list(surveys_path.iterdir()) if surveys_path.exists() else None
+
+    property_group_folders = [
+        p for p in basepath.iterdir() if p.is_dir() and p.name != "Surveys"
+    ]
+
+    for prop in property_group_folders:
+        lasfiles = []
+        for file in [k for k in prop.iterdir() if k.suffix == ".las"]:
+            lasfiles.append(lasio.read(file, mnemonic_case="preserve"))
+        print(f"Importing property group data from to {prop.name}")
+        las_to_drillhole(workspace, lasfiles, dh_group, prop.name, surveys)
+
+    return dh_group
+
+
+if __name__ == "__main__":
+    run(sys.argv[1])

las_geoh5-0.1.0/las_geoh5/import_directories/uijson.py

@@ -0,0 +1,19 @@
+#  Copyright (c) 2023 Mira Geoscience Ltd.
+#
+#  This file is part of las-geoh5 project.
+#
+#  las-geoh5 is distributed under the terms and conditions of the MIT License
+#  (see LICENSE file at the root of this source code package).
+#
+
+from copy import deepcopy
+
+from las_geoh5.export_directories.uijson import ui_json
+
+ui_json = dict(
+    deepcopy(ui_json),
+    **{
+        "title": "LAS file directories to Drillhole group",
+        "run_command": "las_geoh5.import_directories.driver",
+    }
+)

las_geoh5-0.1.0/las_geoh5/import_files/__init__.py

@@ -0,0 +1,7 @@
+#  Copyright (c) 2023 Mira Geoscience Ltd.
+#
+#  This file is part of las-geoh5 project.
+#
+#  las-geoh5 is distributed under the terms and conditions of the MIT License
+#  (see LICENSE file at the root of this source code package).
+#