create bad channels mask, first simple CMake script

python/src/JungfrauCalibration.py

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+from pathlib import Path 
+from aare import JungfrauDataFile
+from helpers import get_first_file
+
+class JungfrauCalibrationParameters: 
+    """
+    A class to hold calibration parameters for the Jungfrau detector.
+    """
+
+    @property 
+    def pedestal_file_dir(self) -> Path:
+        return self._pedestal_file_dir
+
+    @pedestal_file_dir.setter
+    def pedestal_file_dir(self, filepath : Path):
+        if not filepath.exists():
+            raise ValueError(f"Pedestal file directory {filepath} does not exist.")
+        self._pedestal_file_dir = filepath
+
+    @property 
+    def pedestal_g0_file_prefix(self) -> str:
+        return self._pedestal_g0_file_prefix
+
+    @pedestal_g0_file_prefix.setter
+    def pedestal_g0_file_prefix(self, file_prefix : str):
+        self._pedestal_g0_file_prefix = file_prefix
+
+    # TODO: add deprecated decorator 
+    @property
+    def pedestal_file_prefix(self) -> str: 
+        return self._pedestal_file_prefix
+    @pedestal_file_prefix.setter
+    def pedestal_file_prefix(self, file_prefix : str):
+        self._pedestal_file_prefix = file_prefix
+
+    @property
+    def num_pedestals_g0(self) -> int: 
+        return self._num_pedestals_g0
+    
+    @num_pedestals_g0.setter
+    def num_pedestals_g0(self, num_pedestals : int):
+        self._num_pedestals_g0 = num_pedestals
+
+    @property
+    def num_pedestals_g1(self) -> int: 
+        return self._num_pedestals_g1
+    
+    @num_pedestals_g1.setter
+    def num_pedestals_g1(self, num_pedestals : int):
+        self._num_pedestals_g1 = num_pedestals
+
+    @property
+    def num_pedestals_g2(self) -> int: 
+        return self._num_pedestals_g2
+    
+    @num_pedestals_g2.setter
+    def num_pedestals_g2(self, num_pedestals : int):
+        self._num_pedestals_g2 = num_pedestals
+
+    @property
+    def raw_file_dir(self) -> Path:
+        return self._raw_file_dir
+    
+    @raw_file_dir.setter
+    def raw_file_dir(self, filepath : Path):
+        if not filepath.exists():
+            raise ValueError(f"Raw file directory {filepath} does not exist.")
+        self._raw_file_dir = filepath
+
+    @property 
+    def raw_file_prefix(self) -> str:
+        return self._raw_file_prefix
+    
+    @raw_file_prefix.setter
+    def raw_file_prefix(self, file_prefix : str):
+        self._raw_file_prefix = file_prefix
+
+
+    # TODO add a read_config method
+    
+
+def calculate_bad_pixels_mask(calibration_params: JungfrauCalibrationParameters): 
+    """
+    Calculate the bad pixels mask for the Jungfrau detector.
+
+    Returns:
+        np.ndarray: A boolean array where True indicates a bad pixel.
+    """
+
+    if(calibration_params.num_pedestals_g0 is not None and calibration_params.num_pedestals_g1 is not None and calibration_params.num_pedestals_g2 is not None):
+        
+        jungfrau_file = JungfrauDataFile(get_first_file(calibration_params.pedestal_file_dir, calibration_params.pedestal_file_prefix))
+
+        g0_pedestal_frames = jungfrau_file.read_n(calibration_params.num_pedestals_g0) # TODO: option to only read gain? - mmh reading things twice from filesystem also bad 
+
+        g1_pedestal_frames = jungfrau_file.read_n(calibration_params.num_pedestals_g1)
+
+        g2_pedestal_frames = jungfrau_file.read_n(calibration_params.num_pedestals_g2)
+
+
+
+    # Placeholder for actual implementation
+    # This function should analyze the detector data and identify bad pixels
+    pass
+
+
+def main(): 
+    calibration_params = JungfrauCalibrationParameters()
+
+    calibration_params.pedestal_file_dir = Path("/mnt/sls_det_storage/jungfrau_calib/data/Module_708_Calib")
+
+    calibration_params.pedestal_file_prefix = "pedeG0_M708_2025-12-09_"
+    
+    calibration_params.num_pedestals_g0 = 1000
+    calibration_params.num_pedestals_g1 = 1000
+    calibration_params.num_pedestals_g2 = 1000
+
+
+
+
+
+
+
+    

python/src/helpers.py

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+import glob 
+from pathlib import Path 
+
+def get_first_file(path : Path, file_prefix : str): 
+    """
+    Get the first file with lowest index in directory that matches the given prefix.
+    """
+    first_file = min(path.glob(str(Path)+f'{file_prefix}*', default=None)) 
+    if first_file is None:
+        raise ValueError(f"No files found in {path} with prefix {file_prefix}")
+    return first_file