diff --git a/omf/fileio/geoh5.py b/omf/fileio/geoh5.py index bde3291..c2826eb 100644 --- a/omf/fileio/geoh5.py +++ b/omf/fileio/geoh5.py @@ -23,7 +23,6 @@ import numpy as np from geoh5py.data import ( Data, - DataTypeEnum, FloatData, GeometricDataConstants, IntegerData, @@ -33,7 +32,8 @@ ) from geoh5py.groups import ContainerGroup, RootGroup from geoh5py.objects import BlockModel, Curve, Grid2D, ObjectBase, Points, Surface -from geoh5py.shared import FLOAT_NDV, INTEGER_NDV, Entity +from geoh5py.shared import FLOAT_NDV, INTEGER_NDV, DataTypeEnum +from geoh5py.shared.entity import Entity from geoh5py.shared.utils import DEFAULT_PAGE_SIZE from geoh5py.workspace import Workspace @@ -1149,13 +1149,7 @@ def collect_h5_attributes( geometry["axis_u"] = rot.dot(np.c_[1.0, 0.0, 0.0].T).flatten() geometry["axis_v"] = rot.dot(np.c_[0.0, 1.0, 0.0].T).flatten() - geometry.update( - { - "origin": np.r_[ - entity.origin["x"], entity.origin["y"], entity.origin["z"] - ] - } - ) + geometry.update({"origin": entity.origin}) kwargs.update({"geometry": geometry}) return kwargs @@ -1246,13 +1240,7 @@ def collect_h5_attributes( geometry["axis_w"] = np.r_[0, 0, axis[2]] if hasattr(entity, "origin"): - geometry.update( - { - "origin": np.r_[ - entity.origin["x"], entity.origin["y"], entity.origin["z"] - ] - } - ) + geometry.update({"origin": entity.origin}) kwargs.update({"geometry": geometry}) return kwargs diff --git a/omf/fileio/utils.py b/omf/fileio/utils.py index c112853..4bf28d2 100644 --- a/omf/fileio/utils.py +++ b/omf/fileio/utils.py @@ -29,7 +29,6 @@ def compare_elements(elem_a, elem_b): if hasattr(elem_a, "array"): testing.assert_allclose(elem_a.array.array, elem_b.array.array) - if hasattr(elem_a, "data") and elem_a.data: for data_a in elem_a.data: for data_b in elem_b.data: diff --git a/poetry.lock b/poetry.lock index 413e612..ebaefb4 100644 --- a/poetry.lock +++ b/poetry.lock @@ -26,14 +26,14 @@ files = [ [[package]] name = "astroid" -version = "4.0.4" +version = "4.3.3" description = "An abstract syntax tree for Python with inference support." optional = false python-versions = ">=3.10.0" groups = ["dev"] files = [ - {file = "astroid-4.0.4-py3-none-any.whl", hash = "sha256:52f39653876c7dec3e3afd4c2696920e05c83832b9737afc21928f2d2eb7a753"}, - {file = "astroid-4.0.4.tar.gz", hash = "sha256:986fed8bcf79fb82c78b18a53352a0b287a73817d6dbcfba3162da36667c49a0"}, + {file = "astroid-4.3.3-py3-none-any.whl", hash = "sha256:366c99c2907b6407869b1bbfd8abb10f3aea5818309e9c93c9b9c93ecf14bc4f"}, + {file = "astroid-4.3.3.tar.gz", hash = "sha256:d03854b09d92c08e18d8e7d9185d393961186ed0747136d8fcb2d1c008a504ec"}, ] [[package]] @@ -65,105 +65,184 @@ files = [ [[package]] name = "charset-normalizer" -version = "3.4.9" +version = "3.5.2" description = "The Real First Universal Charset Detector. 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a/tests/conftest.py +++ b/tests/conftest.py @@ -24,9 +24,9 @@ def random_project() -> omf.Project: tests_dir = Path(__file__).resolve().parent png_file_path = tests_dir.parent / "docs" / "images" / "PointSetGeometry.png" proj = omf.Project(name="Test project", description="Just some assorted elements") - - vertices = np.repeat(np.arange(1000).reshape(-1, 1), 3, axis=1).astype(float) - values = np.arange(1000).astype(float) + n_values = 5000 + vertices = np.repeat(np.arange(n_values).reshape(-1, 1), 3, axis=1).astype(float) + values = np.arange(n_values).astype(float) pts = omf.PointSetElement( name="Random Points", description="Just random points", diff --git a/tests/convert_volume_test.py b/tests/convert_volume_test.py index 9e3f230..d36d16a 100644 --- a/tests/convert_volume_test.py +++ b/tests/convert_volume_test.py @@ -50,7 +50,7 @@ def test_volume_to_geoh5(tmp_path: Path): omf.MappedData( name="Reference Data", location="cells", - array=np.random.randint(-1, 3, size).flatten().astype(np.int32), + array=np.random.randint(0, 3, size).flatten().astype(np.int32), legends=[ omf.Legend(values=omf.StringArray(array=["abc", "123", "@#$%"])), omf.Legend( @@ -67,7 +67,7 @@ def test_volume_to_geoh5(tmp_path: Path): omf.MappedData( name="Reference Data 2", location="cells", - array=np.random.randint(-1, 3, size).flatten().astype(np.int32), + array=np.random.randint(0, 3, size).flatten().astype(np.int32), legends=[ omf.Legend( values=omf.ColorArray( @@ -137,7 +137,7 @@ def test_volume_flip_origin_z(tmp_path): block_model = workspace.get_entity("vol")[0] assert block_model.z_cell_delimiters[-1] < 0 - assert block_model.origin["z"] == vol.geometry.origin[2] + assert block_model.origin[2] == vol.geometry.origin[2] with Workspace(file) as workspace: rotation = np.random.normal(-180, 180, 1)