update default filenames

src/pygama/evt/modules/geds.py

@@ -20,9 +20,9 @@ def apply_xtalk_correction(
     calibrated_energy_name: str,
     threshold: float = None,
     xtalk_matrix_filename: str,
-    xtalk_rawid_name: str = "xtalk_rawids",
-    xtalk_matrix_name: str = "xtalk_matrix_negative",
-    positive_xtalk_matrix_name: str = "xtalk_matrix_positive",
+    xtalk_rawid_name: str = "xtc/xtalk_rawids",
+    xtalk_matrix_name: str = "xtc/xtalk_matrix_negative",
+    positive_xtalk_matrix_name: str = "xtc/xtalk_matrix_positive",
 ) -> types.VectorOfVectors:
     """Applies the cross-talk correction to the energy observable.
     The format of `xtalk_matrix_filename` should be currently be a path to a lh5 file.

src/pygama/evt/modules/xtalk.py

@@ -6,7 +6,7 @@
 import numpy as np
 from lgdo import lh5
 
-from pygama.lgdo import ls
+from lgdo import ls
 
 from .. import utils
 
@@ -94,9 +94,12 @@ def xtalk_corrected_energy(
     uncalibrated_energies_no_nan = np.nan_to_num(uncalibrated_energies, 0)
     calibrated_energies_no_nan = np.nan_to_num(calibrated_energies, 0)
 
-    energies_threshold = np.where(
-        calibrated_energies_no_nan < threshold, 0, uncalibrated_energies_no_nan
-    )
+    if threshold is not None:
+        energies_threshold = np.where(
+            calibrated_energies_no_nan < threshold, 0, uncalibrated_energies_no_nan
+        )
+    else:
+        energies_threshold = uncalibrated_energies_no_nan
 
     energies_correction = -np.matmul(matrix, energies_threshold.T).T
     return uncalibrated_energies + energies_correction

tests/evt/test_build_evt.py

@@ -123,6 +123,35 @@ def test_field_nesting(lgnd_test_data, files_config):
     assert sorted(evt.sub2.keys()) == ["dummy", "multiplicity"]
 
 
+def test_xtalk(lgnd_test_data,files_config):
+
+    config = {
+        "channels": {"geds_on": ["ch1084803", "ch1084804", "ch1121600"]},
+        "outputs": [
+            "sub1___timestamp",
+            "sub2___multiplicity",
+            "sub2___dummy",
+        ],
+        "operations": {
+            "sub1___timestamp": {
+                "channels": "geds_on",
+                "aggregation_mode": "function",
+                "expression": "pygama.evt.modules.geds.apply_xtalk_correction(<...>,uncalibrated_energy_name='cuspEmax_ctc',calibrated_energy_name=\
+                'cuspEmax_ctc_cal',xtalk_matrix_filename='/data1/users/tdixon/cross_talk/l200-p08-r015-x-talk-matrix_trapTmax.lh5')"
+            }
+        }
+    }
+    build_evt(
+        files_config,
+        config=config,
+        wo_mode="of",
+    )
+
+    outfile = files_config["evt"][0]
+
+    evt = lh5.read("/evt", outfile)
+    show(outfile)
+
 def test_spms_module(lgnd_test_data, files_config):
     build_evt(
         files_config,

tests/evt/test_xtalk.py

@@ -7,7 +7,7 @@ def test_xtalk_corrected_energy():
 
     energy = np.array([[1, 2, 3], [4, 5, 6], [2, 0, 1], [0, 1, 0]])
     matrix = np.array([[0, 0, 1], [1, 0, 2], [0, 2, 0]])
-    energy_corrected_zero_threshold = xtalk.xtalk_corrected_energy(energy, matrix, 0)
+    energy_corrected_zero_threshold = xtalk.xtalk_corrected_energy(energy, energy,matrix, None)
 
     assert np.all(
         energy_corrected_zero_threshold