From 1cc58b6953ae80d2ab6d1650ffe0ecb1e212646d Mon Sep 17 00:00:00 2001
From: Leonardo Schwarz <leonardo.schwarz@fgcz.ethz.ch>
Date: Thu, 5 Sep 2024 16:47:32 +0200
Subject: [PATCH] handle no calibration in the pipeline

---
 .../calibration/perform_calibration.py        |  2 -
 src/depiction/tools/calibrate.py              | 50 ++++++++-----------
 .../app/config_presets/no_calibration.yml     | 23 +++++++++
 3 files changed, 44 insertions(+), 31 deletions(-)
 create mode 100644 src/depiction_targeted_preproc/app/config_presets/no_calibration.yml

diff --git a/src/depiction/calibration/perform_calibration.py b/src/depiction/calibration/perform_calibration.py
index a4328eb..7881bf0 100644
--- a/src/depiction/calibration/perform_calibration.py
+++ b/src/depiction/calibration/perform_calibration.py
@@ -21,12 +21,10 @@ def __init__(
         self,
         calibration: CalibrationMethod,
         parallel_config: ParallelConfig,
-        output_store: h5py.Group | None = None,
         coefficient_output_file: Path | None = None,
     ) -> None:
         self._calibration = calibration
         self._parallel_config = parallel_config
-        self._output_store = output_store
         self._coefficient_output_file = coefficient_output_file
 
     # def _reshape(self, pattern: str, data: DataArray, coordinates) -> DataArray:
diff --git a/src/depiction/tools/calibrate.py b/src/depiction/tools/calibrate.py
index 2c1404f..5a7432a 100644
--- a/src/depiction/tools/calibrate.py
+++ b/src/depiction/tools/calibrate.py
@@ -3,22 +3,21 @@
 from pathlib import Path
 from typing import Literal, Annotated
 
-import h5py
 import numpy as np
 import polars as pl
-from loguru import logger
-from numpy.typing import NDArray
-from pydantic import BaseModel, Field
-
 from depiction.calibration.perform_calibration import PerformCalibration
 from depiction.calibration.spectrum.calibration_method_chemical_peptide_noise import (
     CalibrationMethodChemicalPeptideNoise,
 )
+from depiction.calibration.spectrum.calibration_method_dummy import CalibrationMethodDummy
 from depiction.calibration.spectrum.calibration_method_global_constant_shift import CalibrationMethodGlobalConstantShift
 from depiction.calibration.spectrum.calibration_method_mcc import CalibrationMethodMassClusterCenterModel
 from depiction.calibration.spectrum.calibration_method_regress_shift import CalibrationMethodRegressShift
 from depiction.parallel_ops import ParallelConfig
 from depiction.persistence import ImzmlReadFile, ImzmlWriteFile
+from loguru import logger
+from numpy.typing import NDArray
+from pydantic import BaseModel, Field
 
 
 class CalibrationRegressShiftConfig(BaseModel):
@@ -114,6 +113,8 @@ def get_calibration_instance(config: CalibrationConfig, mass_list: Path | None):
                 model_smoothing_kernel_size=config.method.coef_smoothing_kernel_size,
                 model_smoothing_kernel_std=config.method.coef_smoothing_kernel_std,
             )
+        case None:
+            return CalibrationMethodDummy()
         case _:
             raise NotImplementedError("should be unreachable")
 
@@ -125,27 +126,18 @@ def calibrate(
     mass_list: Path | None = None,
     coefficient_output_path: Path | None = None,
 ) -> None:
-    if config.method is None:
-        logger.info("No calibration requested")
-        input_file.copy_to(output_file.imzml_file)
-        if coefficient_output_path:
-            # TODO not sure if this is the correct action here
-            h5py.File(coefficient_output_path, "w").close()
-    else:
-        calibration = get_calibration_instance(config=config, mass_list=mass_list)
-        parallel_config = ParallelConfig(n_jobs=config.n_jobs)
-        logger.info("Using calibration method: {calibration}", calibration=calibration)
-
-        # TODO is output_store still used
-        perform_calibration = PerformCalibration(
-            calibration=calibration,
-            parallel_config=parallel_config,
-            output_store=None,
-            coefficient_output_file=coefficient_output_path,
-        )
-        perform_calibration.calibrate_image(
-            read_peaks=input_file,
-            write_file=output_file,
-            # TODO:make it possible to customize this
-            read_full=None,
-        )
+    calibration = get_calibration_instance(config=config, mass_list=mass_list)
+    parallel_config = ParallelConfig(n_jobs=config.n_jobs)
+    logger.info("Using calibration method: {calibration}", calibration=calibration)
+
+    perform_calibration = PerformCalibration(
+        calibration=calibration,
+        parallel_config=parallel_config,
+        coefficient_output_file=coefficient_output_path,
+    )
+    perform_calibration.calibrate_image(
+        read_peaks=input_file,
+        write_file=output_file,
+        # TODO:make it possible to customize this
+        read_full=None,
+    )
diff --git a/src/depiction_targeted_preproc/app/config_presets/no_calibration.yml b/src/depiction_targeted_preproc/app/config_presets/no_calibration.yml
new file mode 100644
index 0000000..2fb3854
--- /dev/null
+++ b/src/depiction_targeted_preproc/app/config_presets/no_calibration.yml
@@ -0,0 +1,23 @@
+baseline_correction:
+  baseline_type: TopHat
+  window_size: 3000
+  window_unit: ppm
+pick_peaks:
+  peak_picker:
+    peak_picker_type: FindMFPy
+    int_threshold: 0.0
+  force_peak_picker: no
+  peak_filtering:
+    filters:
+      - method: FilterNHighestIntensityPartitioned
+        max_count: 300
+        n_partitions: 8
+  n_jobs: 10
+filter_peaks:
+  filters:
+    - method: FilterNHighestIntensityPartitioned
+      max_count: 300
+      n_partitions: 8
+calibration:
+  method: null
+  n_jobs: 10