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Streamlined data structure for example files used in context test
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‎tests/client/test_analyser.py‎

Lines changed: 52 additions & 79 deletions
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import pytest
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from murfey.client.analyser import Analyser
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from murfey.client.contexts.atlas import AtlasContext
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from murfey.client.contexts.clem import CLEMContext
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from murfey.client.contexts.fib import FIBContext
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from murfey.client.contexts.spa import SPAContext
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from murfey.client.contexts.spa_metadata import SPAMetadataContext
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from murfey.client.contexts.sxt import SXTContext
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from murfey.client.contexts.tomo import TomographyContext
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from murfey.client.contexts.tomo_metadata import TomographyMetadataContext
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from murfey.util.models import ProcessingParametersSPA, ProcessingParametersTomo
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example_files = [
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# Tomography
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["visit/Position_1_001_0.0_20250715_012434_fractions.tiff", TomographyContext],
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["visit/Position_1_2_002_3.0_20250715_012434_Fractions.mrc", TomographyContext],
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["visit/Position_1_2_003_6.0_20250715_012434_EER.eer", TomographyContext],
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["visit/name1_004_9.0_20250715_012434_fractions.tiff", TomographyContext],
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["visit/Position_1_[30.0].tiff", TomographyContext],
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["visit/Position_1.mdoc", TomographyContext],
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["visit/name1_2.mdoc", TomographyContext],
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# Tomography metadata
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["visit/Session.dm", TomographyMetadataContext],
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["visit/SearchMaps/SearchMap.xml", TomographyMetadataContext],
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["visit/Batch/BatchPositionsList.xml", TomographyMetadataContext],
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["visit/Thumbnails/file.mrc", TomographyMetadataContext],
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# SPA
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["visit/FoilHole_01234_fractions.tiff", SPAContext],
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["visit/FoilHole_01234_EER.eer", SPAContext],
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# SPA metadata
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["atlas/atlas.mrc", AtlasContext],
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["visit/EpuSession.dm", SPAMetadataContext],
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["visit/Metadata/GridSquare.dm", SPAMetadataContext],
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# CLEM LIF file
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["visit/images/test_file.lif", CLEMContext],
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# CLEM TIFF files
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[
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example_files = {
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"CLEMContext": [
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# CLEM LIF file
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"visit/images/test_file.lif",
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# CLEM TIFF files
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"visit/images/2024_03_14_12_34_56--Project001/grid1/Position 12--Z02--C01.tif",
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CLEMContext,
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],
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[
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"visit/images/2024_03_14_12_34_56--Project001/grid1/Position 12_Lng_LVCC--Z02--C01.tif",
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CLEMContext,
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],
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[
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"visit/images/2024_03_14_12_34_56--Project001/grid1/Series001--Z00--C00.tif",
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CLEMContext,
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],
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[
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"visit/images/2024_03_14_12_34_56--Project001/grid1/Series001_Lng_LVCC--Z00--C00.tif",
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CLEMContext,
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],
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# CLEM TIFF file accompanying metadata
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[
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# CLEM TIFF file accompanying metadata
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"visit/images/2024_03_14_12_34_56--Project001/grid1/Metadata/Position 12.xlif",
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CLEMContext,
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],
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[
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"visit/images/2024_03_14_12_34_56--Project001/grid1/Metadata/Position 12_Lng_LVCC.xlif",
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CLEMContext,
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],
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[
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"visit/images/2024_03_14_12_34_56--Project001/grid1/Position 12/Metadata/Position 12_histo.xlif",
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CLEMContext,
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],
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[
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"visit/images/2024_03_14_12_34_56--Project001/grid1/Position 12/Metadata/Position 12_Lng_LVCC_histo.xlif",
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CLEMContext,
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],
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[
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"visit/images/2024_03_14_12_34_56--Project001/grid1/Metadata/Series001.xlif",
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CLEMContext,
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],
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[
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"visit/images/2024_03_14_12_34_56--Project001/grid1/Metadata/Series001_Lng_LVCC.xlif",
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CLEMContext,
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],
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# FIB Autotem files
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["visit/autotem/visit/ProjectData.dat", FIBContext],
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["visit/autotem/visit/Sites/Lamella/SetupImages/Preparation.tif", FIBContext],
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[
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"FIBContext": [
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# FIB Autotem files
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"visit/autotem/visit/ProjectData.dat",
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"visit/autotem/visit/Sites/Lamella/SetupImages/Preparation.tif",
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"visit/autotem/visit/Sites/Lamella (2)//DCImages/DCM_2026-03-09-23-45-40.926/2026-03-09-23-48-43-Finer-Milling-dc_rescan-image-.png",
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FIBContext,
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],
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# FIB Maps files
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["visit/maps/visit/EMproject.emxml", FIBContext],
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[
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# FIB Maps files
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"visit/maps/visit/EMproject.emxml",
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"visit/maps/visit/LayersData/Layer/Electron Snapshot/Electron Snapshot.tiff",
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FIBContext,
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],
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[
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"visit/maps/visit/LayersData/Layer/Electron Snapshot (2)/Electron Snapshot (2).tiff",
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FIBContext,
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],
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# Soft x-ray tomography
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["visit/tomo__tag_ROI10_area1_angle-60to60@1.5_1sec_251p.txrm", SXTContext],
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["visit/X-ray_mosaic_ROI2.xrm", SXTContext],
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]
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"SXTContext": [
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"visit/tomo__tag_ROI10_area1_angle-60to60@1.5_1sec_251p.txrm",
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"visit/X-ray_mosaic_ROI2.xrm",
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],
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"AtlasContext": [
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"atlas/atlas.mrc",
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],
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"TomographyContext": [
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"visit/Position_1_001_0.0_20250715_012434_fractions.tiff",
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"visit/Position_1_2_002_3.0_20250715_012434_Fractions.mrc",
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"visit/Position_1_2_003_6.0_20250715_012434_EER.eer",
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"visit/name1_004_9.0_20250715_012434_fractions.tiff",
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"visit/Position_1_[30.0].tiff",
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"visit/Position_1.mdoc",
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"visit/name1_2.mdoc",
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],
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"TomographyMetadataContext": [
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"visit/Session.dm",
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"visit/SearchMaps/SearchMap.xml",
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"visit/Batch/BatchPositionsList.xml",
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"visit/Thumbnails/file.mrc",
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],
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"SPAContext": [
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"visit/FoilHole_01234_fractions.tiff",
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"visit/FoilHole_01234_EER.eer",
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],
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"SPAMetadataContext": [
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"visit/EpuSession.dm",
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"visit/Metadata/GridSquare.dm",
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],
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}
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@pytest.mark.parametrize("file_and_context", example_files)
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@pytest.mark.parametrize(
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"file_and_context",
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[
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[file, context]
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for context, file_list in example_files.items()
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for file in file_list
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],
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)
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def test_find_context(file_and_context, tmp_path):
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# Unpack parametrised variables
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file_name, context = file_and_context
@@ -111,7 +84,7 @@ def test_find_context(file_and_context, tmp_path):
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# Check that the results are as expected
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assert analyser._find_context(tmp_path / file_name)
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assert isinstance(analyser._context, context)
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assert analyser._context is not None and context in str(analyser._context)
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# Checks for the specific workflow contexts
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if isinstance(analyser._context, TomographyContext):

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