evo-data-converters-ubc 0.1.4__tar.gz

evo_data_converters_ubc-0.1.4/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+*.pyc
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+# C extensions
+*.so
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+# Distribution / packaging
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+# pipenv
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+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
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+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
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+# Celery stuff
+celerybeat-schedule
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+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+example_virtual_env
+env/
+venv/
+ENV/
+env.bak/
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+# Spyder project settings
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+# Rope project settings
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+# mkdocs documentation
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+# mypy
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+# Pyre type checker
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+# Custom
+.idea
+query_results.parquet
+.cache_ggshield
+
+# Object data client caches
+samples/data-converters/python/convert-omf/data/cache
+data/cache
+
+# Development tools
+.vscode/

evo_data_converters_ubc-0.1.4/LICENSE.md

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+   Copyright © 2025 Bentley Systems, Incorporated.
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
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+   See the License for the specific language governing permissions and
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evo_data_converters_ubc-0.1.4/PKG-INFO

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+Metadata-Version: 2.4
+Name: evo-data-converters-ubc
+Version: 0.1.4
+Summary: Python data converters for UBC to Evo geoscience objects
+Project-URL: Source, https://github.com/SeequentEvo/evo-python-sdk
+Project-URL: Tracker, https://github.com/SeequentEvo/evo-python-sdk/issues
+Project-URL: Homepage, https://www.seequent.com/
+Project-URL: Documentation, https://developer.seequent.com/
+Author-email: Seequent <support@seequent.com>
+License-File: LICENSE.md
+Requires-Python: >=3.10
+Requires-Dist: evo-data-converters-common>=0.3.1
+Description-Content-Type: text/markdown
+
+<p align="center"><a href="https://seequent.com" target="_blank"><picture><source media="(prefers-color-scheme: dark)" srcset="https://developer.seequent.com/img/seequent-logo-dark.svg" alt="Seequent logo" width="400" /><img src="https://developer.seequent.com/img/seequent-logo.svg" alt="Seequent logo" width="400" /></picture></a></p>
+<p align="center">
+    <a href="https://pypi.org/project/evo-data-converters-ubc/"><img alt="PyPI - Version" src="https://img.shields.io/pypi/v/evo-data-converters-ubc" /></a>
+    <a href="https://github.com/SeequentEvo/evo-data-converters/actions/workflows/on-merge.yaml"><img src="https://github.com/SeequentEvo/evo-data-converters/actions/workflows/on-merge.yaml/badge.svg" alt="" /></a>
+</p>
+<p align="center">
+    <a href="https://developer.seequent.com/" target="_blank">Seequent Developer Portal</a>
+    &bull; <a href="https://community.seequent.com/group/19-evo" target="_blank">Seequent Community</a>
+    &bull; <a href="https://seequent.com" target="_blank">Seequent website</a>
+</p>
+
+## Evo
+
+Evo is a unified platform for geoscience teams. It enables access, connection, computation, and management of subsurface data. This empowers better decision-making, simplified collaboration, and accelerated innovation. Evo is built on open APIs, allowing developers to build custom integrations and applications. Our open schemas, code examples, and SDK are available for the community to use and extend. 
+
+Evo is powered by Seequent, a Bentley organisation.
+
+## Pre-requisites
+
+* Python 3.10, 3.11, or 3.12
+
+## Installation
+
+```shell
+pip install evo-data-converters-ubc
+```
+
+## UBC
+
+See https://help.seequent.com/Geo/5.0/en-GB/Content/block-models/ubc-grids.htm.
+
+## Usage
+
+For examples of using this package, see the [Jupyter notebooks.](https://github.com/SeequentEvo/evo-data-converters/tree/main/packages/ubc/samples/convert-ubc)
+
+## Code of conduct
+
+We rely on an open, friendly, inclusive environment. To help us ensure this remains possible, please familiarise yourself with our [code of conduct.](https://github.com/SeequentEvo/evo-data-converters/blob/main/CODE_OF_CONDUCT.md)
+
+## License
+Evo data converters are open source and licensed under the [Apache 2.0 license.](https://github.com/SeequentEvo/evo-data-converters/tree/main/packages/ubc/./LICENSE.md)
+
+Copyright © 2025 Bentley Systems, Incorporated.
+
+Licensed under the Apache License, Version 2.0 (the "License").
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

evo_data_converters_ubc-0.1.4/pyproject.toml

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+[project]
+name = "evo-data-converters-ubc"
+description = "Python data converters for UBC to Evo geoscience objects"
+version = "0.1.4"
+requires-python = ">=3.10"
+license-files = ["LICENSE.md"]
+dynamic = ["readme"]
+authors = [
+    { name = "Seequent", email = "support@seequent.com" }
+]
+
+dependencies = [
+    "evo-data-converters-common>=0.3.1",
+]
+
+[project.urls]
+Source = "https://github.com/SeequentEvo/evo-python-sdk"
+Tracker = "https://github.com/SeequentEvo/evo-python-sdk/issues"
+Homepage = "https://www.seequent.com/"
+Documentation = "https://developer.seequent.com/"
+
+[dependency-groups]
+dev = [
+    "pytest",
+]
+
+[tool.ruff]
+src = ["src", "tests"]
+line-length = 120
+
+[build-system]
+requires = ["hatchling", "hatch-fancy-pypi-readme"]
+build-backend = "hatchling.build"
+
+[tool.hatch.build.targets.sdist]
+include = ["src"]
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/evo"]
+
+[tool.hatch.metadata.hooks.fancy-pypi-readme]
+content-type = "text/markdown"
+
+[[tool.hatch.metadata.hooks.fancy-pypi-readme.fragments]]
+path = "README.md"
+
+[[tool.hatch.metadata.hooks.fancy-pypi-readme.substitutions]]
+# Literal TOML strings (single quotes) need no escaping of backslashes.
+# Converts relative links to absolute links in PyPI
+pattern = '\[(.+?)\]\(((?!https?://)\S+?)\)'
+replacement = '[\1](https://github.com/SeequentEvo/evo-data-converters/tree/main/packages/ubc/\g<2>)'

evo_data_converters_ubc-0.1.4/src/evo/data_converters/ubc/__init__.py

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+#  Copyright © 2025 Bentley Systems, Incorporated
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#      http://www.apache.org/licenses/LICENSE-2.0
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.

evo_data_converters_ubc-0.1.4/src/evo/data_converters/ubc/importer/__init__.py

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+#  Copyright © 2025 Bentley Systems, Incorporated
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#      http://www.apache.org/licenses/LICENSE-2.0
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+
+from evo.data_converters.ubc.importer.ubc_reader import UBCFileIOError, UBCInvalidDataError, UBCOOMError
+from evo.data_converters.ubc.importer.ubc_to_evo import convert_ubc
+
+__all__ = ["UBCFileIOError", "UBCInvalidDataError", "UBCOOMError", "convert_ubc"]

evo_data_converters_ubc-0.1.4/src/evo/data_converters/ubc/importer/ubc_reader.py

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+#  Copyright © 2025 Bentley Systems, Incorporated
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#      http://www.apache.org/licenses/LICENSE-2.0
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+
+import contextlib
+import math
+import os
+from collections.abc import Iterator
+from io import TextIOWrapper
+from typing import Any
+
+import numpy
+
+
+class UBCInvalidDataError(Exception):
+    pass
+
+
+class UBCOOMError(Exception):
+    pass
+
+
+class UBCFileIOError(Exception):
+    pass
+
+
+class UBCFile:
+    FILE_TYPE = ""  # this is to be overridden in subclass
+
+    def __init__(self, filename: str):
+        self.filename = filename
+        self.base_filename = os.path.basename(filename)
+        self.line_number_of_import_file: int | None = None
+
+    @contextlib.contextmanager
+    def opened_file(self) -> Iterator[TextIOWrapper]:
+        try:
+            with open(self.filename, "r") as open_file:
+                yield open_file
+        except StopIteration:
+            line_number_msg = (
+                f" after line: {self.line_number_of_import_file:d}" if self.line_number_of_import_file else ""
+            )
+            msg = f"The file '{self.base_filename}' is lacking the expected data{line_number_msg}"
+            raise UBCFileIOError(msg)
+        except OSError as io_error_exception:
+            raise UBCFileIOError(
+                f"An unexpected IO error ({io_error_exception}) occurred while reading the {self.base_filename}"
+            )
+
+    def execute(self, *args: Any, **kwargs: Any) -> Any:
+        try:
+            return self.run(*args, **kwargs)
+        except OSError as exc:
+            raise UBCFileIOError(f"Error reading file: {exc.args[0]}")
+        except MemoryError:
+            raise UBCOOMError(f"Ran out of memory while importing grid file '{self.base_filename}'")
+        except ValueError as value_error_exception:
+            if str(value_error_exception) == "array is too big.":
+                raise UBCOOMError(f"Ran out of memory while importing grid file '{self.base_filename}'")
+            else:
+                line_number = f":{self.line_number_of_import_file:d}" if self.line_number_of_import_file else ""
+                raise UBCInvalidDataError(
+                    f"Error importing the UBC model from the file '{self.base_filename}'{line_number}"
+                )
+        except IndexError:
+            raise UBCInvalidDataError(
+                f"Error importing the UBC model from the file '{self.base_filename}'"
+                "The specified number of cells differs to the number of cell widths given in "
+                "one or more directions"
+            )
+        except Exception as exc:
+            raise UBCFileIOError(f"Error importing the UBC model from '{self.base_filename}'.\n{exc.args[0]}")
+
+    def run(self, *args: Any, **kwargs: Any) -> Any:
+        raise NotImplementedError
+
+
+class UBCMeshFileImporter(UBCFile):
+    FILE_TYPE = "mesh"
+
+    @staticmethod
+    def row_iter(open_file: TextIOWrapper) -> Iterator[tuple[int, list[str]]]:
+        for line_number, line in enumerate(open_file, start=1):
+            yield line_number, line.split()
+
+    @staticmethod
+    def floats_iter(source: list[str]) -> Iterator[float]:
+        for txt in source:
+            pos = txt.find("*")
+            if pos != -1:
+                num = int(txt[:pos])
+                val = float(txt[pos + 1 :])
+                for _ in range(num):
+                    yield val
+            else:
+                yield float(txt)
+
+    def run(self, *args: Any, **kwargs: Any) -> tuple[numpy.ndarray, list[numpy.ndarray], list[int]]:
+        self.line_number_of_import_file = 0
+        with self.opened_file() as data_file:
+            line_iterator = self.row_iter(data_file)
+            self.line_number_of_import_file, line = next(line_iterator)
+            size_of_dimensions = [int(size) for size in line[:3]]  # x, y, z dimensions of grid
+            if 0 in size_of_dimensions:
+                # This is how we do error handling...
+                raise UBCInvalidDataError(f"Invalid size (0) detected in {self.filename}")
+            self.line_number_of_import_file, line = next(line_iterator)
+            origin = numpy.array([float(ordinate) for ordinate in line[:3]])
+            if len(origin) < 3:
+                raise UBCInvalidDataError(f"Invalid origin detected in {self.filename}")
+            spacings = []
+            for size in size_of_dimensions:
+                i = 0
+                d = numpy.zeros((size,), numpy.float64)
+                while i < size:
+                    self.line_number_of_import_file, input_line = next(line_iterator)
+                    for f in self.floats_iter(input_line):
+                        d[i] = f
+                        i += 1
+                spacings.append(d)
+        origin[2] -= sum(spacings[2])
+        spacings[2] = spacings[2][::-1]
+        return origin, spacings, size_of_dimensions
+
+
+class UBCPropertyFileImporter(UBCFile):
+    FILE_TYPE = "property"
+
+    def run(self, n_blocks: int, size_in_blocks: list) -> numpy.ndarray:
+        with self.opened_file() as data_file:
+            values_array = numpy.fromfile(data_file, sep="\n", count=n_blocks)
+
+        if len(values_array) != n_blocks or any(math.isinf(value) or math.isnan(value) for value in values_array):
+            raise UBCInvalidDataError(
+                "Error importing the UBC properties from file: "
+                f"'{self.base_filename}'. "
+                f"The number of property values ({len(values_array)})"
+                f"differs from the number of grid cells ({n_blocks})."
+            )
+        new_shape = tuple(size_in_blocks[:2][::-1] + [size_in_blocks[2]])
+        values_array.shape = new_shape
+        return values_array[:, :, ::-1].swapaxes(0, 1).swapaxes(0, 2).ravel()

evo_data_converters_ubc-0.1.4/src/evo/data_converters/ubc/importer/ubc_to_evo.py

@@ -0,0 +1,79 @@
+#  Copyright © 2025 Bentley Systems, Incorporated
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#      http://www.apache.org/licenses/LICENSE-2.0
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+
+from typing import TYPE_CHECKING, Optional
+
+from evo_schemas.components import BaseSpatialDataProperties_V1_0_1
+
+import evo.logging
+from evo.data_converters.common import (
+    EvoWorkspaceMetadata,
+    create_evo_object_service_and_data_client,
+    publish_geoscience_objects_sync,
+)
+from evo.data_converters.ubc.importer import utils
+from evo.objects.data import ObjectMetadata
+
+logger = evo.logging.getLogger("data_converters")
+
+if TYPE_CHECKING:
+    from evo.notebooks import ServiceManagerWidget
+
+
+def convert_ubc(
+    files_path: list[str],
+    epsg_code: int,
+    evo_workspace_metadata: Optional[EvoWorkspaceMetadata] = None,
+    service_manager_widget: Optional["ServiceManagerWidget"] = None,
+    tags: Optional[dict[str, str]] = None,
+    upload_path: str = "",
+    publish_objects: bool = True,
+    overwrite_existing_objects: bool = False,
+) -> list[BaseSpatialDataProperties_V1_0_1 | ObjectMetadata]:
+    """Converts a UBC files into Geoscience Objects.
+
+    :param files_path: list of paths to the UBC .msh/.nev files.
+    :param epsg_code: The EPSG code to use when creating a Coordinate Reference System object.
+    :param evo_workspace_metadata: (Optional) Evo workspace metadata.
+    :param service_manager_widget: (Optional) Service Manager Widget for use in jupyter notebooks.
+    :param tags: (Optional) Dict of tags to add to the Geoscience Object(s).
+    :param upload_path: (Optional) Path objects will be published under.
+    :publish_objects: (Optional) Set False to return rather than publish objects.
+    :overwrite_existing_objects: (Optional) Set True to overwrite any existing object at the upload_path.
+
+    One of evo_workspace_metadata or service_manager_widget is required.
+
+    Converted objects will be published if either of the following is true:
+    - evo_workspace_metadata.hub_url is present, or
+    - service_manager_widget was passed to this function.
+
+    :return: List of Geoscience Objects, or list of ObjectMetadata if published.
+
+    :raise MissingConnectionDetailsError: If no connections details could be derived.
+    :raise ConflictingConnectionDetailsError: If both evo_workspace_metadata and service_manager_widget present.
+    :raise UBCFileIOError: If failed to read UBC file.
+    :raise UBCInvalidDataError: If an error was detected within the UBC file.
+    :raise UBCOOMError: If out of memory error occurred while handling the UBC file.
+    """
+
+    object_service_client, data_client = create_evo_object_service_and_data_client(
+        evo_workspace_metadata=evo_workspace_metadata, service_manager_widget=service_manager_widget
+    )
+
+    geoscience_objects = [utils.get_geoscience_object_from_ubc(data_client, files_path, epsg_code, tags)]
+    objects_metadata = None
+    if publish_objects:
+        logger.debug("Publishing Geoscience Objects")
+        objects_metadata = publish_geoscience_objects_sync(
+            geoscience_objects, object_service_client, data_client, upload_path, overwrite_existing_objects
+        )
+
+    return objects_metadata if objects_metadata else geoscience_objects

evo_data_converters_ubc-0.1.4/src/evo/data_converters/ubc/importer/utils.py

@@ -0,0 +1,100 @@
+#  Copyright © 2025 Bentley Systems, Incorporated
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#      http://www.apache.org/licenses/LICENSE-2.0
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+
+import os
+from typing import Optional
+
+import numpy
+import pyarrow as pa
+from evo_schemas.components import (
+    ContinuousAttribute_V1_1_0,
+    NanContinuous_V1_0_1,
+    Rotation_V1_1_0,
+)
+from evo_schemas.elements import FloatArray1_V1_0_1
+from evo_schemas.objects import Tensor3DGrid_V1_2_0, Tensor3DGrid_V1_2_0_GridCells3D
+
+import evo.logging
+from evo.data_converters.common import crs_from_epsg_code
+from evo.data_converters.common.utils import get_object_tags, grid_bounding_box
+
+from evo.data_converters.ubc.importer.ubc_reader import UBCMeshFileImporter, UBCPropertyFileImporter
+from evo.objects.utils.data import ObjectDataClient
+
+logger = evo.logging.getLogger("data_converters")
+
+
+def _create_continuous_attributes(
+    data_client: ObjectDataClient, label_to_values: dict
+) -> list[ContinuousAttribute_V1_1_0]:
+    cell_attributes = []
+    for name, values in label_to_values.items():
+        table = pa.table({"values": values})
+        cell_attributes.append(
+            ContinuousAttribute_V1_1_0(
+                name=name,
+                key=name,
+                nan_description=NanContinuous_V1_0_1(values=[]),
+                values=FloatArray1_V1_0_1(**data_client.save_table(table)),
+            )
+        )
+    return cell_attributes
+
+
+def _handle_ubc_files_list(files_path: list[str]) -> tuple[str, list[str]]:
+    ubc_mesh_file: str | None = None
+    ubc_numeric_values_files: list[str] = []
+    for f in files_path:
+        if f.endswith(".msh"):
+            if ubc_mesh_file:
+                raise ValueError("Multiple UBC mesh files provided.")
+            ubc_mesh_file = f
+        else:  # assuming that all other files are numeric values files
+            ubc_numeric_values_files.append(f)
+
+    if not ubc_mesh_file:
+        raise ValueError("No UBC mesh file provided.")
+
+    return ubc_mesh_file, ubc_numeric_values_files
+
+
+def get_geoscience_object_from_ubc(
+    data_client: ObjectDataClient, files_path: list[str], epsg_code: int, tags: Optional[dict[str, str]] = None
+) -> Tensor3DGrid_V1_2_0:
+    ubc_mesh_file, ubc_numeric_values_files = _handle_ubc_files_list(files_path)
+    name = os.path.splitext(os.path.basename(ubc_mesh_file))[0]
+    origin, spacings, size_of_dimensions = UBCMeshFileImporter(ubc_mesh_file).execute()
+
+    n_blocks = size_of_dimensions[0] * size_of_dimensions[1] * size_of_dimensions[2]
+    numerical_values = {}
+    for value_file in ubc_numeric_values_files:
+        values = UBCPropertyFileImporter(value_file).execute(n_blocks, size_of_dimensions)
+        numerical_values[os.path.splitext(os.path.basename(value_file))[0]] = values
+
+    bbox = grid_bounding_box(origin, numpy.identity(3), numpy.array([numpy.sum(d) for d in spacings]))
+    cell_attributes = _create_continuous_attributes(data_client, numerical_values)
+
+    grid_cells_3d = Tensor3DGrid_V1_2_0_GridCells3D(
+        cell_sizes_x=spacings[0].tolist(), cell_sizes_y=spacings[1].tolist(), cell_sizes_z=spacings[2].tolist()
+    )
+
+    return Tensor3DGrid_V1_2_0(
+        name=name,
+        origin=origin.tolist(),
+        size=size_of_dimensions,
+        grid_cells_3d=grid_cells_3d,
+        coordinate_reference_system=crs_from_epsg_code(epsg_code),
+        bounding_box=bbox,
+        rotation=Rotation_V1_1_0(dip_azimuth=0.0, dip=0.0, pitch=0.0),
+        cell_attributes=cell_attributes,
+        uuid=None,
+        tags=get_object_tags(path=os.path.basename(ubc_mesh_file), input_type="UBC", extra_tags=tags),
+    )