Skip to content

frib_trace Module

This module contains the definition of a trace (signal) from the FRIBDAQ, as well as the signal analysis routine.

FribTrace

A single trace from the FRIBDAQ data

Similar to GetTrace, FribTrace represents a raw signal from the SIS3300 module which is managed through the FRIBDAQ. Typically contains signals for the ion chamber (IC), auxillary silicon detectors (Si), and the mesh signal.

Parameters:

Name Type Description Default
data ndarray

The raw trace data

 required
params FribParameters

Configuration parameters controlling the FRIBDAQ signal analysis.

 required

Attributes:

Name Type Description
trace ndarray

The trace data
peaks list[Peak]

The peaks identified in the trace

Methods:

Name Description
FribTrace

Construct the FribTrace and find peaks
set_trace_data

Set the raw trace data and find peaks
is_valid

Check if this trace has valid data
find_peaks

Find peaks in the trace and store the results
get_number_of_peaks

Get the number of peaks found in the trace
get_peaks

Get the found peaks
Source code in src/spyral/trace/frib_trace.py 
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
class FribTrace:
    """A single trace from the FRIBDAQ data

    Similar to GetTrace, FribTrace represents a raw signal from the SIS3300 module which is managed through the FRIBDAQ.
    Typically contains signals for the ion chamber (IC), auxillary silicon detectors (Si), and the mesh signal.

    Parameters
    ----------
    data: ndarray
        The raw trace data
    params: FribParameters
        Configuration parameters controlling the FRIBDAQ signal analysis.

    Attributes
    ----------
    trace: ndarray
        The trace data
    peaks: list[Peak]
        The peaks identified in the trace

    Methods
    -------
    FribTrace(data: ndarray, params: FribParameters)
        Construct the FribTrace and find peaks
    set_trace_data(data: ndarray, params: FribParameters)
        Set the raw trace data and find peaks
    is_valid() -> bool
        Check if this trace has valid data
    find_peaks(params: FribParameters)
        Find peaks in the trace and store the results
    get_number_of_peaks() -> int
        Get the number of peaks found in the trace
    get_peaks() -> list[Peaks]
        Get the found peaks
    """

    def __init__(self, data: np.ndarray, params: FribParameters):
        self.trace: np.ndarray = np.empty(0, dtype=np.int32)
        self.peaks: list[Peak] = []
        self.set_trace_data(data, params)

    def set_trace_data(self, data: np.ndarray, params: FribParameters):
        """Sets the raw trace data and performs peak finding

        Parameters
        ----------
        data: ndarray
            The raw trace data
        params: FribParameters
            Configuration parameters controlling the FRIBDAQ signal analysis.
        """
        if len(data) != FRIB_TRACE_LENGTH:
            raise FribTraceError(
                f"Error at ICTrace, trace was given with length {len(data)}, expected {FRIB_TRACE_LENGTH}"
            )

        self.trace = data.astype(np.int32)
        self.find_peaks(params)

    def is_valid(self) -> bool:
        """Check if this trace has valid data

        Returns
        -------
        bool
            If true, the trace is valid. If false, it isn't
        """
        return len(self.trace) != 0

    def find_peaks(self, params: FribParameters):
        """Find peaks in the trace and store the results

        Peak finding algorithm, similar to used in GetTrace. Uses scipy.signal.find_peaks

        Parameters
        ----------
        params: FribParameters
            Configuration parameters which control the peak finding algorithm
        """

        if not self.is_valid():
            return

        self.peaks.clear()
        pks, props = signal.find_peaks(
            self.trace,
            distance=params.peak_separation,
            prominence=params.peak_prominence,
            width=(0, params.peak_max_width),
            rel_height=0.85,
        )
        for idx, p in enumerate(pks):
            peak = Peak()
            peak.centroid = p
            peak.amplitude = float(self.trace[p])
            peak.positive_inflection = int(np.floor(props["left_ips"][idx]))
            peak.negative_inflection = int(np.ceil(props["right_ips"][idx]))
            peak.integral = np.sum(
                np.abs(self.trace[peak.positive_inflection : peak.negative_inflection])
            )
            if peak.amplitude > params.peak_threshold:
                self.peaks.append(peak)

    def get_number_of_peaks(self) -> int:
        """Get the number of peaks found in the trace

        Returns
        -------
        int
            The number of found peaks
        """
        return len(self.peaks)

    def get_peaks(self) -> list[Peak]:
        """Get the found peaks

        Returns
        -------
        list[Peak]
            The found peaks
        """
        return self.peaks

find_peaks(params)

Find peaks in the trace and store the results

Peak finding algorithm, similar to used in GetTrace. Uses scipy.signal.find_peaks

Parameters:

Name Type Description Default
params FribParameters

Configuration parameters which control the peak finding algorithm

 required
Source code in src/spyral/trace/frib_trace.py 
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
def find_peaks(self, params: FribParameters):
    """Find peaks in the trace and store the results

    Peak finding algorithm, similar to used in GetTrace. Uses scipy.signal.find_peaks

    Parameters
    ----------
    params: FribParameters
        Configuration parameters which control the peak finding algorithm
    """

    if not self.is_valid():
        return

    self.peaks.clear()
    pks, props = signal.find_peaks(
        self.trace,
        distance=params.peak_separation,
        prominence=params.peak_prominence,
        width=(0, params.peak_max_width),
        rel_height=0.85,
    )
    for idx, p in enumerate(pks):
        peak = Peak()
        peak.centroid = p
        peak.amplitude = float(self.trace[p])
        peak.positive_inflection = int(np.floor(props["left_ips"][idx]))
        peak.negative_inflection = int(np.ceil(props["right_ips"][idx]))
        peak.integral = np.sum(
            np.abs(self.trace[peak.positive_inflection : peak.negative_inflection])
        )
        if peak.amplitude > params.peak_threshold:
            self.peaks.append(peak)

get_number_of_peaks()

Get the number of peaks found in the trace

Returns:

Type Description
int

The number of found peaks
Source code in src/spyral/trace/frib_trace.py 
116
117
118
119
120
121
122
123
124
def get_number_of_peaks(self) -> int:
    """Get the number of peaks found in the trace

    Returns
    -------
    int
        The number of found peaks
    """
    return len(self.peaks)

get_peaks()

Get the found peaks

Returns:

Type Description
list[Peak]

The found peaks
Source code in src/spyral/trace/frib_trace.py 
126
127
128
129
130
131
132
133
134
def get_peaks(self) -> list[Peak]:
    """Get the found peaks

    Returns
    -------
    list[Peak]
        The found peaks
    """
    return self.peaks

is_valid()

Check if this trace has valid data

Returns:

Type Description
bool

If true, the trace is valid. If false, it isn't
Source code in src/spyral/trace/frib_trace.py 
72
73
74
75
76
77
78
79
80
def is_valid(self) -> bool:
    """Check if this trace has valid data

    Returns
    -------
    bool
        If true, the trace is valid. If false, it isn't
    """
    return len(self.trace) != 0

set_trace_data(data, params)

Sets the raw trace data and performs peak finding

Parameters:

Name Type Description Default
data ndarray

The raw trace data

 required
params FribParameters

Configuration parameters controlling the FRIBDAQ signal analysis.

 required
Source code in src/spyral/trace/frib_trace.py 
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
def set_trace_data(self, data: np.ndarray, params: FribParameters):
    """Sets the raw trace data and performs peak finding

    Parameters
    ----------
    data: ndarray
        The raw trace data
    params: FribParameters
        Configuration parameters controlling the FRIBDAQ signal analysis.
    """
    if len(data) != FRIB_TRACE_LENGTH:
        raise FribTraceError(
            f"Error at ICTrace, trace was given with length {len(data)}, expected {FRIB_TRACE_LENGTH}"
        )

    self.trace = data.astype(np.int32)
    self.find_peaks(params)