Made sequence parameters editable.

src/quackseq/event.py

@@ -1,6 +1,7 @@
 import logging
 from collections import OrderedDict
 
+from quackseq.pulsesequence import PulseSequence
 from quackseq.pulseparameters import Option
 from quackseq.helpers import UnitConverter
 
@@ -13,26 +14,37 @@ class Event:
     Args:
         name (str): The name of the event
         duration (str): The duration of the event
+        pulse_sequence (PulseSequence): The pulse sequence the event belongs to
 
     Attributes:
         name (str): The name of the event
         duration (str): The duration of the event
-        parameters (OrderedDict): The parameters of the event
+        pulse_sequence (PulseSequence): The pulse sequence the event belongs to
     """
 
-    def __init__(self, name: str, duration: str) -> None:
+    def __init__(self, name: str, duration: str, pulse_sequence : PulseSequence) -> None:
         """Initializes the event."""
         self.parameters = OrderedDict()
         self.name = name
         self.duration = duration
+        self.pulse_sequence = pulse_sequence
+        self.parameters = OrderedDict()
+        self.init_pulse_parameters()
 
-    def add_parameter(self, parameter) -> None:
+    def init_pulse_parameters(self) -> None:
-        """Adds a parameter to the event.
+        """Initializes the pulse parameters of the event."""
-
+        # Create a default instance of the pulse parameter options and add it to the event
-        Args:
+        pulse_parameters = self.pulse_sequence.pulse_parameter_options
-            parameter: The parameter to add
+        for name, pulse_parameter_class in pulse_parameters.items():
-        """
+            logger.debug("Adding pulse parameter %s to event %s", name, self.name)
-        self.parameters.append(parameter)
+            self.parameters[name] = pulse_parameter_class(
+                name
+            )
+            logger.debug(
+                "Created pulse parameter %s with object id %s",
+                name,
+                id(self.parameters[name]),
+            )
 
     def on_duration_changed(self, duration: str) -> None:
         """This method is called when the duration of the event is changed.

src/quackseq/helpers.py

@@ -32,6 +32,8 @@ class UnitConverter:
                 return decimal.Decimal(value)
         except TypeError:
             return decimal.Decimal(value)
+        except decimal.InvalidOperation:
+            raise ValueError(f"Invalid value: {value}, suffixes are n, u, m")
 
     @classmethod
     def to_float(cls, value: str) -> float:

src/quackseq/pulsesequence.py

@@ -2,6 +2,10 @@
 
 import logging
 import importlib.metadata
+from collections import OrderedDict
+
+from quackseq.pulseparameters import PulseParameter, TXPulse, RXReadout
+from quackseq.functions import Function
 
 logger = logging.getLogger(__name__)
 
@@ -11,21 +15,36 @@ class PulseSequence:
 
     Args:
         name (str): The name of the pulse sequence
+        version (str): The version of the pulse sequence
 
     Attributes:
         name (str): The name of the pulse sequence
         events (list): The events of the pulse sequence
+        pulse_parameter_options (dict): The pulse parameter options
     """
 
-    def __init__(self, name, version = None) -> None:
+    def __init__(self, name: str, version: str = None) -> None:
         """Initializes the pulse sequence."""
         self.name = name
-        # Saving version to check for compatability of saved sequence
+        # Saving version to check for compatibility of saved sequence
         if version is not None:
             self.version = version
         else:
-            self.version = importlib.metadata.version("nqrduck_spectrometer")
+            self.version = importlib.metadata.version("quackseq")
+
         self.events = list()
+        self.pulse_parameter_options = OrderedDict()
+
+    def add_pulse_parameter_option(
+        self, name: str, pulse_parameter_class: "PulseParameter"
+    ) -> None:
+        """Adds a pulse parameter option to the spectrometer.
+
+        Args:
+            name (str) : The name of the pulse parameter
+            pulse_parameter_class (PulseParameter) : The pulse parameter class
+        """
+        self.pulse_parameter_options[name] = pulse_parameter_class
 
     def get_event_names(self) -> list:
         """Returns a list of the names of the events in the pulse sequence.
@@ -35,15 +54,27 @@ class PulseSequence:
         """
         return [event.name for event in self.events]
 
-    def add_event(self, event_name: str, duration: float) -> None:
+    def add_event(self, event: "Event") -> None:
         """Add a new event to the pulse sequence.
 
+        Args:
+            event (Event): The event to add
+        """
+        self.events.append(event)
+
+    def create_event(self, event_name: str, duration: float) -> "Event":
+        """Create a new event and return it.
+
         Args:
             event_name (str): The name of the event
             duration (float): The duration of the event
-        """
-        self.events.append(self.Event(event_name, f"{float(duration):.16g}u"))
 
+        Returns:
+            Event: The created event
+        """
+        event = self.Event(event_name, f"{float(duration):.16g}u")
+        self.events.append(event)
+        return event
 
     def delete_event(self, event_name: str) -> None:
         """Deletes an event from the pulse sequence.
@@ -56,6 +87,8 @@ class PulseSequence:
                 self.events.remove(event)
                 break
 
+    # Loading and saving of pulse sequences
+
     def to_json(self):
         """Returns a dict with all the data in the pulse sequence.
 
@@ -63,7 +96,7 @@ class PulseSequence:
             dict: The dict with the sequence data
         """
         # Get the versions of this package
-        data = {"name": self.name, "version" : self.version, "events": []}
+        data = {"name": self.name, "version": self.version, "events": []}
         for event in self.events:
             event_data = {
                 "name": event.name,
@@ -95,7 +128,7 @@ class PulseSequence:
             KeyError: If the pulse parameter options are not the same as the ones in the pulse sequence
         """
         try:
-            obj = cls(sequence["name"], version = sequence["version"])
+            obj = cls(sequence["name"], version=sequence["version"])
         except KeyError:
             logger.error("Pulse sequence version not found")
             raise KeyError("Pulse sequence version not found")
@@ -105,6 +138,7 @@ class PulseSequence:
 
         return obj
 
+    # Automation of pulse sequences
     class Variable:
         """A variable is a parameter that can be used within a pulsesequence as a placeholder.
 
@@ -163,3 +197,68 @@ class PulseSequence:
             if not isinstance(variables, list):
                 raise TypeError("Variables needs to be a list")
             self._variables = variables
+
+
+class QuackSequence(PulseSequence):
+    """This is the Pulse Sequence that is compatible with all types of spectrometers.
+
+    If you want to implement your own spectrometer specific pulse sequence, you can inherit from the PulseSequence class.
+    """
+
+    TX_PULSE = "TXPulse"
+    RX_READOUT = "RXParameters"
+
+    def __init__(self, name: str, version: str = None) -> None:
+        """Initializes the pulse sequence."""
+        super().__init__(name, version)
+
+        self.add_pulse_parameter_option(self.TX_PULSE, TXPulse)
+        self.add_pulse_parameter_option(self.RX_READOUT, RXReadout)
+
+    # TX Specific functions
+
+    def set_tx_amplitude(self, event, amplitude: float) -> None:
+        """Sets the amplitude of the transmitter.
+
+        Args:
+            event (Event): The event to set the amplitude for
+            amplitude (float): The amplitude of the transmitter
+        """
+        event.parameters[self.TX_PULSE].get_option_by_name(
+            TXPulse.RELATIVE_AMPLITUDE
+        ).value = amplitude
+
+    def set_tx_phase(self, event, phase: float) -> None:
+        """Sets the phase of the transmitter.
+
+        Args:
+            event (Event): The event to set the phase for
+            phase (float): The phase of the transmitter
+        """
+        event.parameters[self.TX_PULSE].get_option_by_name(
+            TXPulse.TX_PHASE
+        ).value = phase
+
+    def set_tx_shape(self, event, shape: Function) -> None:
+        """Sets the shape of the transmitter.
+
+        Args:
+            event (Event): The event to set the shape for
+            shape (Any): The shape of the transmitter
+        """
+        event.parameters[self.TX_PULSE].get_option_by_name(
+            TXPulse.TX_PULSE_SHAPE
+        ).value = shape
+
+    # RX Specific functions
+
+    def set_rx(self, event, rx: bool) -> None:
+        """Sets the receiver on or off.
+
+        Args:
+            event (Event): The event to set the receiver for
+            rx (bool): The receiver state
+        """
+        event.parameters[self.RX_READOUT].get_option_by_name(
+            RXReadout.RX
+        ).value = rx

src/quackseq/spectrometer/spectrometer_model.py

@@ -17,11 +17,9 @@ class SpectrometerModel():
 
     Attributes:
         settings (OrderedDict) : The settings of the spectrometer
-        pulse_parameter_options (OrderedDict) : The pulse parameter options of the spectrometer
     """
 
     settings: OrderedDict
-    pulse_parameter_options: OrderedDict
 
     def __init__(self, module):
         """Initializes the spectrometer model.
@@ -31,7 +29,6 @@ class SpectrometerModel():
         """
         super().__init__(module)
         self.settings = OrderedDict()
-        self.pulse_parameter_options = OrderedDict()
 
     def add_setting(self, setting: Setting, category: str) -> None:
         """Adds a setting to the spectrometer.
@@ -62,17 +59,6 @@ class SpectrometerModel():
                     return setting
         raise ValueError(f"Setting with name {name} not found")
 
-    def add_pulse_parameter_option(
-        self, name: str, pulse_parameter_class: "PulseParameter"
-    ) -> None:
-        """Adds a pulse parameter option to the spectrometer.
-
-        Args:
-            name (str) : The name of the pulse parameter
-            pulse_parameter_class (PulseParameter) : The pulse parameter class
-        """
-        self.pulse_parameter_options[name] = pulse_parameter_class
-
     @property
     def target_frequency(self):
         """The target frequency of the spectrometer in Hz. This is the frequency where the magnetic resonance experiment is performed."""

tests/simulator.py

@@ -1,32 +1,40 @@
 # Dummy test to communicate the structure
-from quackseq.pulsesequence import PulseSequence
+from quackseq.pulsesequence import QuackSequence
 from quackseq.event import Event
 from quackseq.functions import RectFunction
 
 
-seq = PulseSequence("test")
+seq = QuackSequence("test")
 
-tx = Event("tx", "10u")
+tx = Event("tx", "10u", seq)
 
-# tx.set_tx_amplitude(1)
+seq.add_event(tx)
-#tx.set_tx_phase(0)
-#tx.set_shape(RectFunction())
 
-#seq.add_event(tx)
+seq.set_tx_amplitude(tx, 1)
+seq.set_tx_phase(tx, 0)
 
-#blank = Event("blank", "10u")
+rect = RectFunction()
 
-#seq.add_event(blank)
+seq.set_tx_shape(tx, rect)
 
-#rx = Event("rx", "10u")
+blank = Event("blank", "10u", seq)
+
+seq.add_event(blank)
+
+rx = Event("rx", "10u", seq)
 #rx.set_rx_phase(0)
-#rx.set_rx(True)
 
-#seq.add_event(rx)
+seq.set_rx(rx, True)
 
-#TR = Event("TR", "1ms")
+seq.add_event(rx)
 
-#seq.add_event(TR)
+TR = Event("TR", "1m", seq)
+
+seq.add_event(TR)
+
+json = seq.to_json()
+
+print(json)
 
 #sim = Simulator()