add the experimental peak picker as an option

src/depiction_targeted_preproc/pipeline_config/model.py

@@ -41,8 +41,19 @@ class PeakPickerMSPeakPicker(BaseModel):
     fit_type: Literal["quadratic"] = "quadratic"
 
 
+class PeakPickerFindMFPy(BaseModel):
+    peak_picker_type: Literal["FindMFPy"]
+    resolution: float = 10000.0
+    width: float = 2.0
+    int_width: float = 2.0
+    int_threshold: float = 10.0
+    area: bool = True
+    max_peaks: int = 0
+
+
 PeakPicker = Annotated[
-    None | PeakPickerBasicInterpolated | PeakPickerMSPeakPicker, Field(discriminator="peak_picker_type")
+    None | PeakPickerBasicInterpolated | PeakPickerMSPeakPicker | PeakPickerFindMFPy,
+    Field(discriminator="peak_picker_type"),
 ]
 
 

src/depiction_targeted_preproc/workflow/proc/pick_peaks.py

@@ -43,6 +43,18 @@ def perform_peak_picking(config: PipelineParameters, read_file: ImzmlReadFile, o
             )
         case model.PeakPickerMSPeakPicker() as peak_picker_config:
             peak_picker = MSPeakPicker(fit_type=peak_picker_config.fit_type, peak_filtering=peak_filtering)
+        case model.PeakPickerFindMFPy() as peak_picker_config:
+            # NOTE: importing this here since it has non-standard dependencies
+            from depiction.spectrum.peak_picking.findmf_peak_picker import FindMFPeakpicker
+
+            peak_picker = FindMFPeakpicker(
+                resolution=peak_picker_config.resolution,
+                width=peak_picker_config.width,
+                int_width=peak_picker_config.int_width,
+                int_threshold=peak_picker_config.int_threshold,
+                area=peak_picker_config.area,
+                max_peaks=peak_picker_config.max_peaks,
+            )
         case _:
             raise ValueError(f"Unsupported peak picker type: {config.peak_picker.peak_picker_type}")
     # TODO correctly detect files which are already picked