call the new cli script from the workflow

src/depiction/tools/cli/correct_baseline.py

@@ -2,10 +2,10 @@
 
 import shutil
 from pathlib import Path
-from typing import Annotated
-from loguru import logger
+from typing import Annotated, Literal
 
 import typer
+from loguru import logger
 from typer import Argument, Option
 
 from depiction.parallel_ops import ParallelConfig
@@ -18,6 +18,8 @@ def correct_baseline(
     output_imzml: Annotated[Path, Argument()],
     n_jobs: Annotated[int, Option()] = None,
     baseline_variant: Annotated[BaselineVariants, Option()] = BaselineVariants.TopHat,
+    window_size: Annotated[int | float, Option()] = 5000,
+    window_unit: Annotated[Literal["ppm", "index"], Option()] = "ppm",
 ) -> None:
     """Removes the baseline from the input imzML file and writes the result to the output imzML file."""
     output_imzml.parent.mkdir(parents=True, exist_ok=True)
@@ -32,7 +34,9 @@ def correct_baseline(
         parallel_config = ParallelConfig(n_jobs=n_jobs)
         input_file = ImzmlReadFile(input_imzml)
         output_file = ImzmlWriteFile(output_imzml, imzml_mode=input_file.imzml_mode)
-        correct_baseline = CorrectBaseline.from_variant(parallel_config=parallel_config, variant=baseline_variant)
+        correct_baseline = CorrectBaseline.from_variant(
+            parallel_config=parallel_config, variant=baseline_variant, window_size=window_size, window_unit=window_unit
+        )
         correct_baseline.evaluate_file(input_file, output_file)
 
 

src/depiction/tools/correct_baseline.py

@@ -1,11 +1,9 @@
 from __future__ import annotations
 
 import enum
-from pathlib import Path
 from typing import TYPE_CHECKING, Literal
 
 import numpy as np
-import typer
 
 from depiction.parallel_ops.parallel_config import ParallelConfig
 from depiction.parallel_ops.write_spectra_parallel import WriteSpectraParallel
@@ -20,7 +18,6 @@
 
 if TYPE_CHECKING:
     from numpy.typing import NDArray
-    from pathlib import Path
     from depiction.spectrum.baseline.baseline import Baseline
 
 
@@ -97,25 +94,3 @@ def _get_baseline_correction(variant: BaselineVariants):
             return LocalMediansBaseline(window_size=5000, window_unit="ppm")
         else:
             raise ValueError(f"Unknown baseline variant: {variant}")
-
-
-# TODO testing
-# TODO use it in the workflow
-# TODO replace use by tools.cli.correct_baseline
-def main(
-    input_imzml: Path,
-    output_imzml: Path,
-    n_jobs: int = 20,
-    baseline_variant: BaselineVariants = BaselineVariants.TopHat,
-) -> None:
-    """Corrects the baseline of `input_imzml` and writes the results to `output_imzml`."""
-    parallel_config = ParallelConfig(n_jobs=n_jobs, task_size=None)
-    input_file = ImzmlReadFile(input_imzml)
-    output_file = ImzmlWriteFile(output_imzml, imzml_mode=input_file.imzml_mode)
-    output_imzml.parent.mkdir(exist_ok=True, parents=True)
-    correct_baseline = CorrectBaseline.from_variant(parallel_config=parallel_config, variant=baseline_variant)
-    correct_baseline.evaluate_file(input_file, output_file)
-
-
-if __name__ == "__main__":
-    typer.run(main)

src/depiction_targeted_preproc/workflow/proc/correct_baseline.py

@@ -1,41 +1,41 @@
-import shutil
 from pathlib import Path
 from typing import Annotated
-import typer
-from loguru import logger
 
-from depiction.spectrum.baseline.tophat_baseline import TophatBaseline
-from depiction.parallel_ops import ParallelConfig
-from depiction.persistence import ImzmlReadFile, ImzmlWriteFile
-from depiction.tools.correct_baseline import CorrectBaseline
+import typer
 
+from depiction.tools.cli.correct_baseline import correct_baseline
+from depiction.tools.correct_baseline import BaselineVariants
 from depiction_targeted_preproc.pipeline_config.model import PipelineParameters, BaselineAdjustmentTophat
 
 
-def correct_baseline(
+def proc_correct_baseline(
     input_imzml_path: Annotated[Path, typer.Option()],
     config_path: Annotated[Path, typer.Option()],
     output_imzml_path: Annotated[Path, typer.Option()],
 ) -> None:
     config = PipelineParameters.parse_yaml(config_path)
+    window = {}
     match config.baseline_adjustment:
         case None:
-            logger.info("Baseline adjustment is deactivated")
-            shutil.copy(input_imzml_path, output_imzml_path)
-            shutil.copy(input_imzml_path.with_suffix(".ibd"), output_imzml_path.with_suffix(".ibd"))
+            baseline_variant = BaselineVariants.Zero
         case BaselineAdjustmentTophat(window_size=window_size, window_unit=window_unit):
-            baseline = TophatBaseline(window_size=window_size, window_unit=window_unit)
-            parallel_config = ParallelConfig(n_jobs=config.n_jobs, task_size=None)
-            read_file = ImzmlReadFile(input_imzml_path)
-            write_file = ImzmlWriteFile(output_imzml_path, imzml_mode=read_file.imzml_mode)
-            correct_baseline = CorrectBaseline(parallel_config=parallel_config, baseline_correction=baseline)
-            correct_baseline.evaluate_file(read_file, write_file)
+            baseline_variant = BaselineVariants.TopHat
+            window["window_size"] = window_size
+            window["window_unit"] = window_unit
         case _:
             raise ValueError(f"Unsupported baseline adjustment type: {config.baseline_adjustment.baseline_type}")
 
+    correct_baseline(
+        input_imzml=input_imzml_path,
+        output_imzml=output_imzml_path,
+        n_jobs=config.n_jobs,
+        baseline_variant=baseline_variant,
+        **window,
+    )
+
 
 def main() -> None:
-    typer.run(correct_baseline)
+    typer.run(proc_correct_baseline)
 
 
 if __name__ == "__main__":