From 735d4ebfb9f9abdfc0f549ee7395223c8d735b42 Mon Sep 17 00:00:00 2001
From: Ryan Roussel <rroussel@slac.stanford.edu>
Date: Mon, 29 Jan 2024 14:52:25 -0600
Subject: [PATCH 1/7] create measurement class and io function

---
 lcls_tools/common/io.py                      | 13 +++++++++++++
 lcls_tools/common/measurement/__init__.py    |  0
 lcls_tools/common/measurement/measurement.py | 17 +++++++++++++++++
 3 files changed, 30 insertions(+)
 create mode 100644 lcls_tools/common/io.py
 create mode 100644 lcls_tools/common/measurement/__init__.py
 create mode 100644 lcls_tools/common/measurement/measurement.py

diff --git a/lcls_tools/common/io.py b/lcls_tools/common/io.py
new file mode 100644
index 00000000..56483c9d
--- /dev/null
+++ b/lcls_tools/common/io.py
@@ -0,0 +1,13 @@
+from typing import Union
+
+from lcls_tools.common.devices.device import Device
+
+
+def dump_data_to_h5py(
+        element: Union[Device, Measurement],
+        data: dict,
+        filename: str = None
+):
+    """
+    Dump data to
+    """
\ No newline at end of file
diff --git a/lcls_tools/common/measurement/__init__.py b/lcls_tools/common/measurement/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/lcls_tools/common/measurement/measurement.py b/lcls_tools/common/measurement/measurement.py
new file mode 100644
index 00000000..d94ebe55
--- /dev/null
+++ b/lcls_tools/common/measurement/measurement.py
@@ -0,0 +1,17 @@
+from abc import ABC, abstractmethod
+from typing import Optional
+
+from pydantic import BaseModel, DirectoryPath
+
+
+class Measurement(BaseModel, ABC):
+    name: str
+    device_list: list[str]
+    save_data: bool = True
+    save_location: Optional[DirectoryPath] = None
+
+    @abstractmethod
+    def measure(self) -> dict:
+        """ Implements a measurement and returns a dictionary with the results"""
+        pass
+

From 1dc398ebce3620e2255cf460630b5b809dcd2ce1 Mon Sep 17 00:00:00 2001
From: Ryan Roussel <rroussel@slac.stanford.edu>
Date: Mon, 29 Jan 2024 15:08:54 -0600
Subject: [PATCH 2/7] change python function to object

---
 lcls_tools/common/io.py | 26 ++++++++++++++++----------
 1 file changed, 16 insertions(+), 10 deletions(-)

diff --git a/lcls_tools/common/io.py b/lcls_tools/common/io.py
index 56483c9d..f70d7d4b 100644
--- a/lcls_tools/common/io.py
+++ b/lcls_tools/common/io.py
@@ -1,13 +1,19 @@
-from typing import Union
+from typing import Optional
 
-from lcls_tools.common.devices.device import Device
+from lcls_tools.common.measurement.measurement import Measurement
 
 
-def dump_data_to_h5py(
-        element: Union[Device, Measurement],
-        data: dict,
-        filename: str = None
-):
-    """
-    Dump data to
-    """
\ No newline at end of file
+class HDF5Dumper:
+    def __init__(self):
+        pass
+
+    def dump_data_to_file(
+            self,
+            measurement_data: dict,
+            measurement_obj: Measurement,
+            filename: Optional[str] = None
+    ):
+        """
+        Dump data to h5file
+        """
+        pass

From 70005818c8b27278226f9ba9e25d2ce7d8ce55b9 Mon Sep 17 00:00:00 2001
From: Ryan Roussel <rroussel@slac.stanford.edu>
Date: Mon, 29 Jan 2024 15:20:12 -0600
Subject: [PATCH 3/7] implement basic ICT monitor

---
 lcls_tools/common/devices/ict.py              | 35 +++++++++++++++++++
 .../{measurement => measurements}/__init__.py |  0
 lcls_tools/common/measurements/beam_charge.py | 11 ++++++
 .../measurement.py                            |  1 -
 4 files changed, 46 insertions(+), 1 deletion(-)
 create mode 100644 lcls_tools/common/devices/ict.py
 rename lcls_tools/common/{measurement => measurements}/__init__.py (100%)
 create mode 100644 lcls_tools/common/measurements/beam_charge.py
 rename lcls_tools/common/{measurement => measurements}/measurement.py (93%)

diff --git a/lcls_tools/common/devices/ict.py b/lcls_tools/common/devices/ict.py
new file mode 100644
index 00000000..7efd03dd
--- /dev/null
+++ b/lcls_tools/common/devices/ict.py
@@ -0,0 +1,35 @@
+from pydantic import field_validator, SerializeAsAny
+
+from lcls_tools.common.devices.device import Device, PVSet, ControlInformation, Metadata
+from epics import PV
+
+
+class ICTPVSet(PVSet):
+    """
+    The PV interface for screens is not uniform.
+    We list the potential PVs below and only
+    use the ones that are set to be PV-typed after
+    initialisation.
+    """
+
+    charge_nC: PV
+
+    def __init__(self, **kwargs):
+        super().__init__(**kwargs)
+
+    @field_validator("*", mode="before")
+    def validate_pv_fields(cls, v: str):
+        """Convert each PV string from YAML into a PV object"""
+        return PV(v)
+
+
+class ICTControlInformation(ControlInformation):
+    PVs: SerializeAsAny[ICTPVSet]
+
+
+class ICT(Device):
+    controls_information: SerializeAsAny[ICTControlInformation]
+    metadata: SerializeAsAny[Metadata]
+
+    def get_charge(self) -> float:
+        return self.controls_information.PVs.charge_nC.get(as_numpy=True)
diff --git a/lcls_tools/common/measurement/__init__.py b/lcls_tools/common/measurements/__init__.py
similarity index 100%
rename from lcls_tools/common/measurement/__init__.py
rename to lcls_tools/common/measurements/__init__.py
diff --git a/lcls_tools/common/measurements/beam_charge.py b/lcls_tools/common/measurements/beam_charge.py
new file mode 100644
index 00000000..edc81964
--- /dev/null
+++ b/lcls_tools/common/measurements/beam_charge.py
@@ -0,0 +1,11 @@
+from lcls_tools.common.devices.ict import ICT
+from lcls_tools.common.measurements.measurement import Measurement
+
+
+class BeamChargeMeasurement(Measurement):
+    name = "beam_charge"
+    ict_monitor: ICT
+
+    def measure(self) -> dict:
+        return {"bunch_charge_nC": self.ict_monitor.get_charge()}
+
diff --git a/lcls_tools/common/measurement/measurement.py b/lcls_tools/common/measurements/measurement.py
similarity index 93%
rename from lcls_tools/common/measurement/measurement.py
rename to lcls_tools/common/measurements/measurement.py
index d94ebe55..a42a984f 100644
--- a/lcls_tools/common/measurement/measurement.py
+++ b/lcls_tools/common/measurements/measurement.py
@@ -6,7 +6,6 @@
 
 class Measurement(BaseModel, ABC):
     name: str
-    device_list: list[str]
     save_data: bool = True
     save_location: Optional[DirectoryPath] = None
 

From f8cc57357050be731b342a559d40076ae1194b39 Mon Sep 17 00:00:00 2001
From: Ryan Roussel <rroussel@slac.stanford.edu>
Date: Wed, 31 Jan 2024 09:28:34 -0600
Subject: [PATCH 4/7] rename IO object, fix ict docstring

---
 lcls_tools/common/devices/ict.py |  1 -
 lcls_tools/common/io.py          | 17 +++++++++++++----
 2 files changed, 13 insertions(+), 5 deletions(-)

diff --git a/lcls_tools/common/devices/ict.py b/lcls_tools/common/devices/ict.py
index 7efd03dd..12f96946 100644
--- a/lcls_tools/common/devices/ict.py
+++ b/lcls_tools/common/devices/ict.py
@@ -6,7 +6,6 @@
 
 class ICTPVSet(PVSet):
     """
-    The PV interface for screens is not uniform.
     We list the potential PVs below and only
     use the ones that are set to be PV-typed after
     initialisation.
diff --git a/lcls_tools/common/io.py b/lcls_tools/common/io.py
index f70d7d4b..792ece01 100644
--- a/lcls_tools/common/io.py
+++ b/lcls_tools/common/io.py
@@ -1,19 +1,28 @@
 from typing import Optional
 
-from lcls_tools.common.measurement.measurement import Measurement
+from lcls_tools.common.measurements.measurement import Measurement
 
 
-class HDF5Dumper:
+class HDF5IO:
     def __init__(self):
         pass
 
-    def dump_data_to_file(
+    def write(
             self,
             measurement_data: dict,
             measurement_obj: Measurement,
             filename: Optional[str] = None
     ):
         """
-        Dump data to h5file
+        Write data to h5file
+        """
+        pass
+
+    def read(
+            self,
+            filename: Optional[str] = None
+    ):
+        """
+        Read data from h5file
         """
         pass

From 8167a54e61161753c972bc1771a7563c0869e5b4 Mon Sep 17 00:00:00 2001
From: Ryan Roussel <rroussel@slac.stanford.edu>
Date: Wed, 31 Jan 2024 13:36:31 -0600
Subject: [PATCH 5/7] replace pass with NotImplementedError

---
 lcls_tools/common/io.py                       | 4 ++--
 lcls_tools/common/measurements/measurement.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/lcls_tools/common/io.py b/lcls_tools/common/io.py
index 792ece01..73fb61d6 100644
--- a/lcls_tools/common/io.py
+++ b/lcls_tools/common/io.py
@@ -16,7 +16,7 @@ def write(
         """
         Write data to h5file
         """
-        pass
+        raise NotImplementedError
 
     def read(
             self,
@@ -25,4 +25,4 @@ def read(
         """
         Read data from h5file
         """
-        pass
+        raise NotImplementedError
diff --git a/lcls_tools/common/measurements/measurement.py b/lcls_tools/common/measurements/measurement.py
index a42a984f..4933ff52 100644
--- a/lcls_tools/common/measurements/measurement.py
+++ b/lcls_tools/common/measurements/measurement.py
@@ -12,5 +12,5 @@ class Measurement(BaseModel, ABC):
     @abstractmethod
     def measure(self) -> dict:
         """ Implements a measurement and returns a dictionary with the results"""
-        pass
+        raise NotImplementedError
 

From 0948fb3bf191f9ae15e9b6db68d596d396a5cbe8 Mon Sep 17 00:00:00 2001
From: Ryan Roussel <rroussel@slac.stanford.edu>
Date: Wed, 14 Feb 2024 14:34:18 -0600
Subject: [PATCH 6/7] adds multi-shot capabilities and averaging to the ICT
 example measurement class

---
 lcls_tools/common/measurements/beam_charge.py | 45 ++++++++++++++++++-
 lcls_tools/common/measurements/measurement.py |  2 +-
 lcls_tools/common/measurements/utils.py       | 12 +++++
 3 files changed, 56 insertions(+), 3 deletions(-)
 create mode 100644 lcls_tools/common/measurements/utils.py

diff --git a/lcls_tools/common/measurements/beam_charge.py b/lcls_tools/common/measurements/beam_charge.py
index edc81964..8925adde 100644
--- a/lcls_tools/common/measurements/beam_charge.py
+++ b/lcls_tools/common/measurements/beam_charge.py
@@ -1,11 +1,52 @@
+import numpy as np
+from pydantic import PositiveFloat
+
 from lcls_tools.common.devices.ict import ICT
 from lcls_tools.common.measurements.measurement import Measurement
+import time
+
+from lcls_tools.common.measurements.utils import calculate_statistics
 
 
 class BeamChargeMeasurement(Measurement):
     name = "beam_charge"
     ict_monitor: ICT
+    wait_time: PositiveFloat = 1.0
+
+    def measure(self, n_shots: int = 1) -> dict:
+        """
+        Measure the bunch charge using an ICT monitor.
+
+        Parameters:
+        - n_shots (int, optional): The number of measurements to perform. Defaults to 1.
+
+        Returns:
+        dict: A dictionary containing the measured bunch charge values and additional
+        statistics if multiple shots are taken.
+
+        If n_shots is 1, the function returns a dictionary with the key "bunch_charge_nC"
+        and the corresponding single measurement value.
+
+        If n_shots is greater than 1, the function performs multiple measurements with
+        the specified wait time and returns a dictionary with the key "bunch_charge_nC"
+        containing a list of measured values. Additionally, statistical information
+        (mean, standard deviation, etc.) is included in the dictionary.
+
+
+        """
+        if n_shots == 1:
+            return {"bunch_charge_nC": self.ict_monitor.get_charge()}
+        elif n_shots > 1:
+            bunch_charges = []
+            for i in range(n_shots):
+                bunch_charges += [self.ict_monitor.get_charge()]
+                time.sleep(self.wait_time)
+
+            # add statistics to results
+            results = {"bunch_charge_nC": bunch_charges}
+            results = results | calculate_statistics(
+                np.array(bunch_charges), "bunch_charge_nC"
+            )
 
-    def measure(self) -> dict:
-        return {"bunch_charge_nC": self.ict_monitor.get_charge()}
+            return results
 
diff --git a/lcls_tools/common/measurements/measurement.py b/lcls_tools/common/measurements/measurement.py
index 4933ff52..c1722374 100644
--- a/lcls_tools/common/measurements/measurement.py
+++ b/lcls_tools/common/measurements/measurement.py
@@ -10,7 +10,7 @@ class Measurement(BaseModel, ABC):
     save_location: Optional[DirectoryPath] = None
 
     @abstractmethod
-    def measure(self) -> dict:
+    def measure(self, **kwargs) -> dict:
         """ Implements a measurement and returns a dictionary with the results"""
         raise NotImplementedError
 
diff --git a/lcls_tools/common/measurements/utils.py b/lcls_tools/common/measurements/utils.py
new file mode 100644
index 00000000..88915adb
--- /dev/null
+++ b/lcls_tools/common/measurements/utils.py
@@ -0,0 +1,12 @@
+import numpy as np
+from numpy import ndarray
+
+
+def calculate_statistics(data: ndarray, name):
+    return {
+        f"{name}_mean": np.mean(data),
+        f"{name}_std": np.std(data),
+        f"{name}_q05": np.quantile(data, 0.05),
+        f"{name}_q95": np.quantile(data, 0.95),
+    }
+

From eb03c33c744c1d55e6c0be07d0581497ff497020 Mon Sep 17 00:00:00 2001
From: Ryan Roussel <rroussel@slac.stanford.edu>
Date: Tue, 20 Feb 2024 22:15:06 -0600
Subject: [PATCH 7/7] fixes to pass flake8

---
 lcls_tools/common/measurements/beam_charge.py | 1 -
 lcls_tools/common/measurements/measurement.py | 1 -
 lcls_tools/common/measurements/utils.py       | 1 -
 3 files changed, 3 deletions(-)

diff --git a/lcls_tools/common/measurements/beam_charge.py b/lcls_tools/common/measurements/beam_charge.py
index 8925adde..adfcd0f7 100644
--- a/lcls_tools/common/measurements/beam_charge.py
+++ b/lcls_tools/common/measurements/beam_charge.py
@@ -49,4 +49,3 @@ def measure(self, n_shots: int = 1) -> dict:
             )
 
             return results
-
diff --git a/lcls_tools/common/measurements/measurement.py b/lcls_tools/common/measurements/measurement.py
index c1722374..3917c3d1 100644
--- a/lcls_tools/common/measurements/measurement.py
+++ b/lcls_tools/common/measurements/measurement.py
@@ -13,4 +13,3 @@ class Measurement(BaseModel, ABC):
     def measure(self, **kwargs) -> dict:
         """ Implements a measurement and returns a dictionary with the results"""
         raise NotImplementedError
-
diff --git a/lcls_tools/common/measurements/utils.py b/lcls_tools/common/measurements/utils.py
index 88915adb..d5198891 100644
--- a/lcls_tools/common/measurements/utils.py
+++ b/lcls_tools/common/measurements/utils.py
@@ -9,4 +9,3 @@ def calculate_statistics(data: ndarray, name):
         f"{name}_q05": np.quantile(data, 0.05),
         f"{name}_q95": np.quantile(data, 0.95),
     }
-