Addition of CalibrationWriterNectarCAM tool for writing Category A calibration files (#207)

* Add script to obtain metadata of `ctapipe` and `nectarchain`. Taken from `lstcam_calib` with minor adaptations for `nectarchain`.

* added group name as option to HDF5 readout, particularly useful for pedestal output files that use various groups to store data

* first attempt for a Tool that writes a category A output file from NectarCAM containers

* Add example script for the usage of the CalibrationWriterNectarCAM tool

* ensure that filled arrays have the correct type (based on `lstcam_calib` example file)

* do one-padding instead of zero-padding to expand arrays related to pixel status with missing pixels (so a missing pixel = True for those that are added, i.e. due that were not included due to hardware failure)

* fixed hardware failing pixel status bug

Author: pcorcam

src/nectarchain/data/container/core.py

@@ -54,7 +54,9 @@ class NectarCAMContainer(Container):
     """
 
     @staticmethod
-    def _container_from_hdf5(path, container_class, index_component=0):
+    def _container_from_hdf5(
+        path, container_class, index_component=0, group_name="data"
+    ):
         """Static method to read a container from an HDF5 file.
 
         Parameters:
@@ -74,15 +76,17 @@ def _container_from_hdf5(path, container_class, index_component=0):
         container = container_class()
         with HDF5TableReader(path) as reader:
             tableReader = reader.read(
-                table_name=f"/data/{container_class.__name__}_{index_component}",
+                table_name=(
+                    f"/{group_name}/{container_class.__name__}_{index_component}"
+                ),
                 containers=container_class,
             )
             container = next(tableReader)
 
         yield container
 
     @classmethod
-    def from_hdf5(cls, path, index_component=0):
+    def from_hdf5(cls, path, index_component=0, group_name="data"):
         """Reads a container from an HDF5 file.
 
         Parameters:
@@ -99,7 +103,10 @@ def from_hdf5(cls, path, index_component=0):
         """
 
         return cls._container_from_hdf5(
-            path, container_class=cls, index_component=index_component
+            path,
+            container_class=cls,
+            index_component=index_component,
+            group_name=group_name,
         )
 
 

src/nectarchain/data/container/gain_container.py

@@ -43,7 +43,7 @@ class GainContainer(NectarCAMContainer):
     pixels_id = Field(type=np.ndarray, dtype=np.uint16, ndim=1, description="pixel ids")
 
     @classmethod
-    def from_hdf5(cls, path):
+    def from_hdf5(cls, path, group_name="data"):
         """Class method to read a GainContainer from an HDF5 file.
 
         Args:
@@ -52,7 +52,9 @@ def from_hdf5(cls, path):
         Yields:
             GainContainer: The container from the data in the HDF5 file.
         """
-        return super(__class__, cls)._container_from_hdf5(path, container_class=cls)
+        return super(__class__, cls)._container_from_hdf5(
+            path, container_class=cls, group_name=group_name
+        )
 
 
 class SPEfitContainer(GainContainer):