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ENH: update idc-index-data to add AdmittingDiagnosis (#136)
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fedorov authored Oct 18, 2024
1 parent b0c3e28 commit 8f7743e
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14 changes: 8 additions & 6 deletions docs/column_descriptions.md
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Expand Up @@ -65,16 +65,18 @@ with slide microscopy data.
was collected
- `primaryAnatomicStructureModifier`: additional characteristics of the
specimen, such as whether it is a tumor or normal tissue
- `admittingDiagnosis`: if available, diagnosis of the patient; populated
using the first item of the `AdmittingDiagnosesSequence` in DICOM SM series
- `illuminationType`: specifies the type of illumination used when obtaining
the image

In case of `embeddingMedium`, `tissueFixative`, `staining_usingSubstance`,
`primaryAnatomicStructure`, `primaryAnatomicStructureModifier` and
`illuminationType` the attributes exist with suffix `_code_designator_value_str`
and `_CodeMeaning`, which indicates whether the column contains
CodeSchemeDesignator and CodeValue, or CodeMeaning. If this is new to you, a
brief explanation on the three-value based coding scheme in DICOM can be found
at https://learn.canceridc.dev/dicom/coding-schemes.
`primaryAnatomicStructure`, `primaryAnatomicStructureModifier`,
`admittingDiagnosis` and `illuminationType` the attributes exist with suffix
`_code_designator_value_str` and `_CodeMeaning`, which indicates whether the
column contains CodeSchemeDesignator and CodeValue, or CodeMeaning. If this is
new to you, a brief explanation on the three-value based coding scheme in DICOM
can be found at https://learn.canceridc.dev/dicom/coding-schemes.

## `sm_instance_index`

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2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -34,7 +34,7 @@ dynamic = ["version"]
dependencies = [
"click",
'duckdb>=0.10.0,<1.1.0',
"idc-index-data==19.0.2",
"idc-index-data==19.0.3",
"packaging",
"pandas<2.2",
"platformdirs",
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