From dd97388fe9d342350539ac31b2a8dd99e6996f34 Mon Sep 17 00:00:00 2001 From: domfournier Date: Wed, 29 Jul 2026 10:01:51 -0700 Subject: [PATCH 1/3] Transpose the colormap values --- omf/fileio/geoh5.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/omf/fileio/geoh5.py b/omf/fileio/geoh5.py index 84d857d..84d8887 100644 --- a/omf/fileio/geoh5.py +++ b/omf/fileio/geoh5.py @@ -847,7 +847,7 @@ def collect_h5_attributes( Legend(values=StringArray(array=labels)), Legend( values=ColorArray( - array=element.entity_type.color_map.values[ # type: ignore + array=element.entity_type.color_map.values.T[ # type: ignore 1:-1, ind: ] .astype(int) @@ -922,9 +922,9 @@ def collect_h5_attributes( if getattr(element.entity_type, "color_map", None) is not None: cmap = element.entity_type.color_map # type: ignore ind = np.argsort(cmap.values[0, :]) - values = cmap.values[0, ind] + values = cmap.values.T[0, ind] limits = [values[0], values[-1]] - colors = cmap.values[1:-1, ind] # Drop val and alpha + colors = cmap.values.T[1:-1, ind] # Drop val and alpha if colors.shape[1] != 128: new_vals = np.linspace(limits[0], limits[1], 128) From 244f269fd50baeca1aed739b1dc4a2086e745fbc Mon Sep 17 00:00:00 2001 From: domfournier Date: Wed, 29 Jul 2026 14:30:44 -0700 Subject: [PATCH 2/3] Transpose color array from start --- omf/fileio/geoh5.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/omf/fileio/geoh5.py b/omf/fileio/geoh5.py index 84d8887..bde3291 100644 --- a/omf/fileio/geoh5.py +++ b/omf/fileio/geoh5.py @@ -921,10 +921,12 @@ def collect_h5_attributes( with fetch_active_workspace(workspace): if getattr(element.entity_type, "color_map", None) is not None: cmap = element.entity_type.color_map # type: ignore - ind = np.argsort(cmap.values[0, :]) - values = cmap.values.T[0, ind] + + array = cmap.values.T + ind = np.argsort(array[0, :]) + values = array[0, ind] limits = [values[0], values[-1]] - colors = cmap.values.T[1:-1, ind] # Drop val and alpha + colors = array[1:-1, ind] # Drop val and alpha if colors.shape[1] != 128: new_vals = np.linspace(limits[0], limits[1], 128) From 8390c9ac45cceeb7384188291c690607a41296bd Mon Sep 17 00:00:00 2001 From: domfournier Date: Wed, 29 Jul 2026 14:32:46 -0700 Subject: [PATCH 3/3] Update lock file --- poetry.lock | 473 +++++++++++++++++++++++----------------------------- 1 file changed, 211 insertions(+), 262 deletions(-) diff --git a/poetry.lock b/poetry.lock index 140f040..413e612 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 2.4.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.3.2 and should not be changed by hand. [[package]] name = "alabaster" @@ -14,14 +14,14 @@ files = [ [[package]] name = "annotated-types" -version = "0.7.0" +version = "0.8.0" description = "Reusable constraint types to use with typing.Annotated" optional = false -python-versions = ">=3.8" +python-versions = ">=3.10" groups = ["main"] files = [ - {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"}, - {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"}, + {file = "annotated_types-0.8.0-py3-none-any.whl", hash = "sha256:f072f4d804ea359e4eaf198b1af7a8b0943881a87f31bb764f8bf219bb9419e0"}, + {file = "annotated_types-0.8.0.tar.gz", hash = "sha256:13b2beaad985e05e2d6407ee4c4f35590b11f8d693a258a561055cac8f64cab7"}, ] [[package]] @@ -53,153 +53,117 @@ dev = ["backports.zoneinfo ; python_version < \"3.9\"", "freezegun (>=1.0,<2.0)" [[package]] name = "certifi" -version = "2026.5.20" +version = "2026.7.22" description = "Python package for providing Mozilla's CA Bundle." optional = false python-versions = ">=3.7" groups = ["dev"] files = [ - {file = "certifi-2026.5.20-py3-none-any.whl", hash = "sha256:3c52e209ba0a4ad7aebe60436a4ab349c39e1e602e8c134221e546902ad25897"}, - {file = "certifi-2026.5.20.tar.gz", hash = "sha256:69dea482ab64caa7b9f6aba1c6bf48bb6a5448d1c0f1b17ab42ad8c763a5344d"}, + {file = "certifi-2026.7.22-py3-none-any.whl", hash = "sha256:62f22742b58a1a33014a2b6b706588a8d7e2a88ae7bd1a6ebe8c992928483775"}, + {file = "certifi-2026.7.22.tar.gz", hash = "sha256:741e2c3b351ddf169a738da9f2c048608ff7f2c5cc02f1ebc6b118bb090d5d55"}, ] [[package]] name = "charset-normalizer" -version = "3.4.7" +version = "3.4.9" description = "The Real First Universal Charset Detector. 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