From bea8240ac99132fe11a04597b7e4f3c0b82cb544 Mon Sep 17 00:00:00 2001
From: Leonardo Schwarz <leonardo.schwarz@fgcz.ethz.ch>
Date: Tue, 12 Nov 2024 09:38:16 +0100
Subject: [PATCH] generate a config with smoothing deactivated

---
 ...re_calibration_config_with_no_smoothing.py | 38 +++++++++++++++++++
 .../workflow/experimental.smk                 | 10 +++++
 2 files changed, 48 insertions(+)
 create mode 100644 src/depiction_targeted_preproc/workflow/exp/prepare_calibration_config_with_no_smoothing.py

diff --git a/src/depiction_targeted_preproc/workflow/exp/prepare_calibration_config_with_no_smoothing.py b/src/depiction_targeted_preproc/workflow/exp/prepare_calibration_config_with_no_smoothing.py
new file mode 100644
index 0000000..71bbbbd
--- /dev/null
+++ b/src/depiction_targeted_preproc/workflow/exp/prepare_calibration_config_with_no_smoothing.py
@@ -0,0 +1,38 @@
+import cyclopts
+import yaml
+from pathlib import Path
+
+from depiction.tools.calibrate.config import (
+    CalibrationConfig,
+    CalibrationRegressShiftConfig,
+    CalibrationChemicalPeptideNoiseConfig,
+    CalibrationMCCConfig,
+    CalibrationConstantGlobalShiftConfig,
+)
+
+app = cyclopts.App()
+
+
+def remove_smoothing(config: CalibrationConfig) -> CalibrationConfig:
+    match config:
+        case CalibrationRegressShiftConfig():
+            return config.model_copy(update={"spatial_smoothing": None})
+        case CalibrationChemicalPeptideNoiseConfig():
+            return config
+        case CalibrationMCCConfig():
+            return config.model_copy(update={"coef_smoothing_activated": False})
+        case CalibrationConstantGlobalShiftConfig():
+            return config
+        case _:
+            raise NotImplementedError(f"Smoothing removal for {config.method.calibration_method} not implemented.")
+
+
+@app.default
+def prepare(input_config_path: Path, output_config_path: Path) -> None:
+    config = CalibrationConfig.model_validate(yaml.safe_load(input_config_path.read_text()))
+    config_new = remove_smoothing(config)
+    output_config_path.write_text(yaml.safe_dump(config_new.model_dump(mode="json")))
+
+
+if __name__ == "__main__":
+    app()
diff --git a/src/depiction_targeted_preproc/workflow/experimental.smk b/src/depiction_targeted_preproc/workflow/experimental.smk
index 540a42f..f0873e4 100644
--- a/src/depiction_targeted_preproc/workflow/experimental.smk
+++ b/src/depiction_targeted_preproc/workflow/experimental.smk
@@ -99,3 +99,13 @@ rule exp_plot_map_comparison:
 #        " --input-mass-shift-path {input.mass_shift}"
 #        " --output-pdf-path {output.pdf}"
 #
+
+
+rule exp_prepare_calibration_config_with_no_smoothing:
+    input:
+        config="{sample}/config/proc_calibrate.yml",
+    output:
+        config="{sample}/config/proc_calibrate_no_smoothing.yml",
+    shell:
+        "python -m depiction_targeted_preproc.workflow.exp.prepare_calibration_config_with_no_smoothing"
+        " --input-config-path {input.config} --output-config-path {output.config}"