Autopipeline utils
autopipeline_utils
#
Utility functions for the autopipeline module.
Functions:
Name | Description |
---|---|
save_pipeline_reports |
Save pipeline reports including success/failure reports and simplified index. |
PipelineResults
dataclass
#
PipelineResults(
successful_results: typing.List[
imgtools.autopipeline_utils.ResultType
],
failed_results: typing.List[
imgtools.autopipeline_utils.ResultType
],
all_results: typing.List[
imgtools.autopipeline_utils.ResultType
],
timestamp: str | None = None,
)
Bases: typing.Generic[imgtools.autopipeline_utils.ResultType]
Class to store and handle pipeline processing results.
This class stores successful and failed results from processing samples through the autopipeline and provides methods for saving reports and generating summary statistics.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
|
typing.List[imgtools.autopipeline_utils.ResultType]
|
List of successful processing results |
required |
|
typing.List[imgtools.autopipeline_utils.ResultType]
|
List of failed processing results |
required |
|
typing.List[imgtools.autopipeline_utils.ResultType]
|
List of all processing results |
required |
|
str
|
Timestamp for this run, by default current datetime |
None
|
Methods:
Name | Description |
---|---|
log_summary |
Log summary information about the results. |
to_dict |
Convert results to a dictionary. |
log_summary
#
Log summary information about the results.
Source code in src/imgtools/autopipeline_utils.py
to_dict
#
to_dict() -> typing.Dict[
str,
typing.List[imgtools.autopipeline_utils.ResultType],
]
save_pipeline_reports
#
save_pipeline_reports(
results: imgtools.autopipeline_utils.PipelineResults,
index_file: "Path",
root_dir_name: str,
simplified_columns: typing.List[str],
index_lock_check_func: (
typing.Callable[[], "Path"] | None
) = None,
) -> typing.Dict[str, "Path"]
Save pipeline reports including success/failure reports and simplified index.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
|
imgtools.autopipeline_utils.PipelineResults
|
The pipeline results to save |
required |
|
pathlib.Path
|
Path to the index file |
required |
|
str
|
Name of the root directory for output |
required |
|
typing.List[str]
|
List of columns to include in the simplified index |
required |
|
callable
|
Function to check and remove index lock file |
None
|
Returns:
Type | Description |
---|---|
typing.Dict[str, pathlib.Path]
|
Dictionary of saved file paths |
Source code in src/imgtools/autopipeline_utils.py
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