OSSpectrum#

class pyopenms.OSSpectrum#

Bases: object

Cython implementation of _OSSpectrum

Original C++ documentation is available here

__init__()#

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: OSSpectrum) → None

Methods

`__init__`
`get_data_arrays`	Get all data arrays associated with the spectrum.
`get_drift_time_array`	Get the drift time array of the spectrum as a numpy array (copy).
`get_drift_time_array_mv`	Get the drift time array of the spectrum as a memory view (no copy).
`get_intensity_array`	Get the intensity array of the spectrum as a numpy array (copy).
`get_intensity_array_mv`	Get the intensity array of the spectrum as a memory view (no copy).
`get_mz_array`	Get the m/z array of the spectrum as a numpy array (copy).
`get_mz_array_mv`	Get the m/z array of the spectrum as a memory view (no copy).
`set_data_arrays`	Set all data arrays for the spectrum.
`set_intensity_array`	Set the intensity array for the spectrum.
`set_mz_array`	Set the m/z array (mass-to-charge ratios) for the spectrum.

get_data_arrays()#

Get all data arrays associated with the spectrum.

This includes the m/z array, intensity array, drift time array (if present), and any additional meta data arrays that may be present in the spectrum.

Returns:

list: A list of OSBinaryDataArray objects containing all data arrays: associated with this spectrum.

Example:

>>> spectrum = OSSpectrum()
>>> data_arrays = spectrum.get_data_arrays()
>>> print(f"Number of data arrays: {len(data_arrays)}")
>>> for i, array in enumerate(data_arrays):
...     data = array.get_data()
...     if data is not None:
...         print(f"Array {i}: {len(data)} data points")

get_drift_time_array()#

Get the drift time array of the spectrum as a numpy array (copy).

This method is used for ion mobility spectrometry data where each peak has an associated drift time value.

Returns:

np.ndarray or None: A 1D numpy array (float64) containing the drift time values: for each peak in the spectrum, or None if no drift time data is available.

Example:

>>> spectrum = OSSpectrum()
>>> drift_times = spectrum.get_drift_time_array()
>>> if drift_times is not None:
...     print(f"Drift time range: {min(drift_times)} - {max(drift_times)} ms")
... else:
...     print("No drift time data available")

get_drift_time_array_mv()#

Get the drift time array of the spectrum as a memory view (no copy).

This method provides direct access to the underlying drift time data without copying, which is more memory efficient for large ion mobility datasets.

Returns:

memoryview or None: A memory view of the drift time values: for each peak in the spectrum, or None if no drift time data is available.

Warning:

DO NOT store the returned memory view for later use after the spectrum object goes out of scope, as this will lead to undefined behavior and potential crashes.

Example:

>>> spectrum = OSSpectrum()
>>> drift_mv = spectrum.get_drift_time_array_mv()
>>> if drift_mv is not None:
...     # CORRECT: Use immediately
...     avg_drift = sum(drift_mv) / len(drift_mv)
...
>>> # WRONG: Don't do this!
>>> # stored_mv = spectrum.get_drift_time_array_mv()
>>> # del spectrum  # Memory view now points to invalid memory!
>>> # if stored_mv: print(stored_mv[0])  # Undefined behavior/crash

get_intensity_array()#

Get the intensity array of the spectrum as a numpy array (copy).

Returns:

np.ndarray: A 1D numpy array (float64) containing the intensity values: for each peak in the spectrum.

Example:

>>> spectrum = OSSpectrum()
>>> intensities = spectrum.get_intensity_array()
>>> print(f"Base peak intensity: {max(intensities)}")
>>> # Safe to modify the returned array
>>> normalized = intensities / max(intensities)  # This won't affect the original data

get_intensity_array_mv()#

Get the intensity array of the spectrum as a memory view (no copy).

This method provides direct access to the underlying data without copying, which is more memory efficient for large datasets.

Returns:

memoryview: A memory view of the intensity values: for each peak in the spectrum, or None if empty.

Warning:

DO NOT store the returned memory view for later use after the spectrum object goes out of scope, as this will lead to undefined behavior and potential crashes.

Example:

>>> spectrum = OSSpectrum()
>>> intensities_mv = spectrum.get_intensity_array_mv()
>>> # CORRECT: Use immediately for calculations
>>> total_intensity = sum(intensities_mv)
>>>
>>> # WRONG: Don't do this!
>>> # stored_mv = spectrum.get_intensity_array_mv()
>>> # del spectrum  # Memory view now points to invalid memory!
>>> # print(sum(stored_mv))  # Undefined behavior/crash

get_mz_array()#

Get the m/z array of the spectrum as a numpy array (copy).

Returns:

np.ndarray: A 1D numpy array (float64) containing the mass-to-charge ratio values: for each peak in the spectrum.

Example:

>>> spectrum = OSSpectrum()
>>> mz_values = spectrum.get_mz_array()
>>> print(f"m/z range: {min(mz_values)} - {max(mz_values)}")
>>> # Safe to modify the returned array
>>> mz_values += 0.001  # This won't affect the original data

get_mz_array_mv()#

Get the m/z array of the spectrum as a memory view (no copy).

This method provides direct access to the underlying data without copying, which is more memory efficient for large datasets.

Returns:

memoryview: A memory view of the mass-to-charge ratio values: for each peak in the spectrum, or None if empty.

Warning:

DO NOT store the returned memory view for later use after the spectrum object goes out of scope, as this will lead to undefined behavior and potential crashes.

Example:

>>> spectrum = OSSpectrum()
>>> mz_mv = spectrum.get_mz_array_mv()
>>> # CORRECT: Use immediately
>>> min_mz = min(mz_mv)
>>>
>>> # WRONG: Don't do this!
>>> # stored_mv = spectrum.get_mz_array_mv()
>>> # del spectrum  # Memory view now points to invalid memory!
>>> # print(stored_mv[0])  # Undefined behavior/crash

set_data_arrays()#

Set all data arrays for the spectrum.

This method replaces all existing data arrays with the provided ones. The input should include m/z array, intensity array, and any additional meta data arrays (such as drift time arrays for ion mobility data).

Args:

inp (list): A list of OSBinaryDataArray objects to set as the: spectrum’s data arrays.

Raises:

AssertionError: If inp is not a list or contains elements that are: not OSBinaryDataArray instances.

Example:

>>> spectrum = OSSpectrum()
>>> mz_array = OSBinaryDataArray()
>>> intensity_array = OSBinaryDataArray()
>>> # ... populate arrays with data ...
>>> spectrum.set_data_arrays([mz_array, intensity_array])

set_intensity_array()#

Set the intensity array for the spectrum.

Args:

data (list): A list of numeric values representing the intensity values: for each peak in the spectrum. The length should match the m/z array length.

Raises:

AssertionError: If data is not a list.

Example:

>>> spectrum = OSSpectrum()
>>> intensities = [1000.0, 5000.0, 3000.0, 2000.0, 1500.0]
>>> spectrum.set_intensity_array(intensities)
>>> # Make sure length matches m/z array
>>> assert len(intensities) == len(spectrum.get_mz_array())

set_mz_array()#

Set the m/z array (mass-to-charge ratios) for the spectrum.

Args:

data (list): A list of numeric values representing the m/z values: for each peak in the spectrum. Values should typically be in ascending order for proper spectrum processing.

Raises:

AssertionError: If data is not a list.

Example:

>>> spectrum = OSSpectrum()
>>> mz_values = [100.05, 200.10, 300.15, 400.20, 500.25]
>>> spectrum.set_mz_array(mz_values)