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ENH: update idc-index-data to add AdmittingDiagnosis (#136)
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docs/column_descriptions.md

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@@ -65,16 +65,18 @@ with slide microscopy data.
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was collected
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- `primaryAnatomicStructureModifier`: additional characteristics of the
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specimen, such as whether it is a tumor or normal tissue
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- `admittingDiagnosis`: if available, diagnosis of the patient; populated
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using the first item of the `AdmittingDiagnosesSequence` in DICOM SM series
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- `illuminationType`: specifies the type of illumination used when obtaining
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the image
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In case of `embeddingMedium`, `tissueFixative`, `staining_usingSubstance`,
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`primaryAnatomicStructure`, `primaryAnatomicStructureModifier` and
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`illuminationType` the attributes exist with suffix `_code_designator_value_str`
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and `_CodeMeaning`, which indicates whether the column contains
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CodeSchemeDesignator and CodeValue, or CodeMeaning. If this is new to you, a
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brief explanation on the three-value based coding scheme in DICOM can be found
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at https://learn.canceridc.dev/dicom/coding-schemes.
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`primaryAnatomicStructure`, `primaryAnatomicStructureModifier`,
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`admittingDiagnosis` and `illuminationType` the attributes exist with suffix
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`_code_designator_value_str` and `_CodeMeaning`, which indicates whether the
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column contains CodeSchemeDesignator and CodeValue, or CodeMeaning. If this is
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new to you, a brief explanation on the three-value based coding scheme in DICOM
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can be found at https://learn.canceridc.dev/dicom/coding-schemes.
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## `sm_instance_index`
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pyproject.toml

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dependencies = [
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"click",
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'duckdb>=0.10.0,<1.1.0',
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"idc-index-data==19.0.2",
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"idc-index-data==19.0.3",
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"packaging",
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"pandas<2.2",
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"platformdirs",

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