Merge branch 'feat/Extra_data_pnCCD' into 'master'

[pnCCD] [CORRECT][DARK] EXtra-data, processing using pasha, and parallel correction for different sequence files.

See merge request detectors/pycalibration!559

src/cal_tools/pnccdlib.py

-# Extracting slow data:
-import os
-import traceback
-from typing import Tuple
-
-import h5py
-
 VALID_GAINS = {
-    "a" : 1.0,
-    "b" : 4.0,
-    "c" : 16.0,
-    "d" : 64.0,
-    "e" : 256.0,
-    "f" : 340.0,
-    "g" : 512.0
+    "a": 1.0,
+    "b": 4.0,
+    "c": 16.0,
+    "d": 64.0,
+    "e": 256.0,
+    "f": 340.0,
+    "g": 512.0
 }
 
 
-def extract_slow_data(karabo_id: str, karabo_da_control: str,
-                      ctrl_fname: str, ctrl_path: str,
-                      mdl_ctrl_path: str,
-                      bias_voltage: float, gain: float,
-                      fix_temperature_top :float,
-                      fix_temperature_bot :float,
-                      ) -> Tuple[float, float, float, float]:
-    """
-    Extract slow data from given control paths.
-    """
-    try:
-        with h5py.File(ctrl_fname, "r") as f:
-            if bias_voltage == 0.:
-                bias_voltage = abs(f[os.path.join(mdl_ctrl_path,
-                                                  "DAQ_MPOD/u0voltage/value")][0])  # noqa
-            if gain == 0.1:
-                gain = f[os.path.join(mdl_ctrl_path,
-                                      "DAQ_GAIN/pNCCDGain/value")][0]
-            if fix_temperature_top == 0.:
-                fix_temperature_top = f[os.path.join(ctrl_path,
-                                                     "inputA/krdg/value")][0]
-            if fix_temperature_bot == 0.:
-                fix_temperature_bot = f[os.path.join(ctrl_path,
-                                                     "inputB/krdg/value")][0]
-    except IOError:
-        print("Error during reading slow data,"
-              " please check the given h5 path for the control parameters")
-        traceback.print_exc(limit=1)
-        print("bias voltage control h5path:",
-              os.path.join(mdl_ctrl_path, "DAQ_MPOD/u0voltage/value"))
-        print("gain control h5path:",
-              os.path.join(mdl_ctrl_path, "DAQ_GAIN/pNCCDGain/value"))
-        print("fix_temperature_top control h5path:",
-              os.path.join(ctrl_path, "inputA/krdg/value"))
-        print("fix_temperature_bot control h5path:",
-              os.path.join(ctrl_path, "inputB/krdg/value"))
+class PnccdCtrl():
+    def __init__(
+        self,
+        run_dc: "extra_data.DataCollection",  # noqa
+        karabo_id: str
+    ):
+        """ Extract control data from given control paths.
+        :param run_dc: run Extra-data data collection.
+        :param karabo_id: Detector identifier name.
+        """
+        self.run_dc = run_dc
+        self.ctrl_src = f"{karabo_id}/CTRL/TCTRL"
+        self.mdl_src_temp = f"{karabo_id}/MDL/{{}}"
+
+    def get_bias_voltage(self):
+        return(
+            abs(self.run_dc.get_run_value(
+                self.mdl_src_temp.format("DAQ_MPOD"), "u0voltage.value")))
+
+    def get_gain(self):
+        return(
+            self.run_dc.get_run_value(
+                self.mdl_src_temp.format("DAQ_GAIN"), "pNCCDGain.value"))
+
+    def get_fix_temperature_top(self):
+        return self.run_dc.get_run_value(self.ctrl_src, "inputA.krdg.value")
 
-    return bias_voltage, gain, fix_temperature_top, fix_temperature_bot
+    def get_fix_temperature_bot(self):
+        return self.run_dc.get_run_value(self.ctrl_src, "inputB.krdg.value")

src/xfel_calibrate/notebooks.py

@@ -120,8 +120,9 @@ notebooks = {
         },
         "CORRECT": {
             "notebook": "notebooks/pnCCD/Correct_pnCCD_NBC.ipynb",
-            "concurrency": {"parameter": None,
-                            "default concurrency": None,
+            "concurrency": {"parameter": "sequences",
+                            "default concurrency": [-1],
+                            "use function": "balance_sequences",
                             "cluster cores": 32},
         },
     },