`pyms.IonChromatogram`

Classes to model a GC-MS Ion Chromatogram.

Classes:

`BasePeakChromatogram`(intensity_list, time_list)	Models a base peak chromatogram (BPC).
`ExtractedIonChromatogram`(intensity_list, …)	Models an extracted ion chromatogram (EIC).
`IonChromatogram`(intensity_list, time_list[, …])	Models an ion chromatogram.

class BasePeakChromatogram(intensity_list, time_list)[source]

Bases: IonChromatogram

Models a base peak chromatogram (BPC).

An ion chromatogram is a set of intensities as a function of retention time. This can can be either m/z channel intensities (for example, ion chromatograms at m/z = 65), or cumulative intensities over all measured m/z. In the latter case the ion chromatogram is total ion chromatogram (TIC).

Parameters

intensity_list (Union[Sequence[float], ndarray]) – Ion chromatogram intensity values
time_list (Sequence[float]) – A list of ion chromatogram retention times

Authors

Lewis Lee, Vladimir Likic, Dominic Davis-Foster (type assertions and properties)

New in version 2.3.0.

Methods:

`__copy__`()	Returns a new IonChromatogram containing a copy of the data in this object.
`__eq__`(other)	Return whether this IonChromatogram object is equal to another object.
`__len__`()	Returns the length of the IonChromatogram object.
`__sub__`(other)	Subtracts another IC from the current one (in place).
`dump`(file_name[, protocol])	Dumps an object to a file through `pickle.dump()`.
`get_index_at_time`(time)	Returns the nearest index corresponding to the given time.
`get_intensity_at_index`(ix)	Returns the intensity at the given index.
`get_time_at_index`(ix)	Returns time at given index.
`is_bpc`()	Returns whether the ion chromatogram is a base peak chromatogram (BPC).
`is_eic`()	Returns whether the ion chromatogram is an extracted ion chromatogram (EIC).
`is_tic`()	Returns whether the ion chromatogram is a total ion chromatogram (TIC) or extracted ion chromatogram (EIC).
`write`(file_name[, minutes, formatting])	Writes the ion chromatogram to the specified file.

Attributes:

`intensity_array`	Returns a copy of the intensity array.
`intensity_array_list`	Returns a copy of the intensity array as a list of lists of floats.
`intensity_matrix`	Returns a copy of the intensity matrix.
`mass`	Returns the m/z channel of the IC.
`matrix_list`	Returns the intensity matrix as a list of lists of floats.
`time_list`	Returns a copy of the time list.
`time_step`	Returns the time step.

__copy__()

Returns a new IonChromatogram containing a copy of the data in this object.

Return type: IonChromatogram

__eq__(other)

Return whether this IonChromatogram object is equal to another object.

Parameters: other (Any) – The other object to test equality with.
Return type: bool

__len__()

Returns the length of the IonChromatogram object.

Authors: Lewis Lee, Vladimir Likic
Return type: int

__sub__(other)

Subtracts another IC from the current one (in place).

Parameters: other (IonChromatogram) – Another IC
Return type: IonChromatogram

dump(file_name, protocol=3)

Dumps an object to a file through pickle.dump().

Parameters

file_name (Union[str, Path, PathLike]) – Filename to save the dump as.
protocol (int) – The pickle protocol to use. Default 3.

Authors

Vladimir Likic, Dominic Davis-Foster (pathlib and pickle protocol support)

get_index_at_time(time)

Returns the nearest index corresponding to the given time.

Parameters: time (float) – Time in seconds
Return type: int
Returns: Nearest index corresponding to given time
Authors: Lewis Lee, Tim Erwin, Vladimir Likic

Changed in version 2.3.0: Now returns -1 if no index is found.

get_intensity_at_index(ix)

Returns the intensity at the given index.

Parameters: ix (int) – An index.
Authors: Lewis Lee, Vladimir Likic
Return type: float

get_time_at_index(ix)

Returns time at given index.

Parameters: ix (int)
Authors: Lewis Lee, Vladimir Likic
Return type: float

property intensity_array

Returns a copy of the intensity array.

Return type: ndarray
Returns: Matrix of intensity values.
Authors: Andrew Isaac, Lewis Lee

property intensity_array_list

Returns a copy of the intensity array as a list of lists of floats.

Return type: List[List[float]]
Returns: Matrix of intensity values.
Author: Andrew Isaac

property intensity_matrix

Returns a copy of the intensity matrix.

Return type: ndarray
Returns: Matrix of intensity values.
Author: Andrew Isaac

static is_bpc()[source]

Returns whether the ion chromatogram is a base peak chromatogram (BPC).

Return type: bool

static is_eic()

Returns whether the ion chromatogram is an extracted ion chromatogram (EIC).

New in version 2.3.0.

Return type: bool

is_tic()

Returns whether the ion chromatogram is a total ion chromatogram (TIC) or extracted ion chromatogram (EIC).

Authors: Lewis Lee, Vladimir Likic
Return type: bool

property mass

Returns the m/z channel of the IC.

Author: Sean O’Callaghan
Return type: Optional[float]

property matrix_list

Returns the intensity matrix as a list of lists of floats.

Return type: ndarray
Returns: Matrix of intensity values
Author: Andrew Isaac

property time_list

Returns a copy of the time list.

Return type: List[float]
Returns: List of retention times
Authors: Andrew Isaac, Lewis Lee, Vladimir Likic

property time_step

Returns the time step.

Authors: Lewis Lee, Vladimir Likic
Return type: float

write(file_name, minutes=False, formatting=True)

Writes the ion chromatogram to the specified file.

Parameters

file_name (Union[str, Path, PathLike]) – The name of the output file
minutes (bool) – A boolean value indicating whether to write time in minutes. Default False.
formatting (bool) – Whether to format the numbers in the output. Default True.

Authors

Lewis Lee, Vladimir Likic, Dominic Davis-Foster (pathlib support)

class ExtractedIonChromatogram(intensity_list, time_list, masses)[source]

Bases: IonChromatogram

Models an extracted ion chromatogram (EIC).

An ion chromatogram is a set of intensities as a function of retention time. This can can be either m/z channel intensities (for example, ion chromatograms at m/z = 65), or cumulative intensities over all measured m/z. In the latter case the ion chromatogram is total ion chromatogram (TIC).

Parameters

intensity_list (Union[Sequence[float], ndarray]) – Ion chromatogram intensity values
time_list (Sequence[float]) – A list of ion chromatogram retention times
masses (Sequence[float]) – List of extracted masses in the EIC.

Authors

Lewis Lee, Vladimir Likic, Dominic Davis-Foster (type assertions and properties)

New in version 2.3.0.

Methods:

`__copy__`()	Returns a new IonChromatogram containing a copy of the data in this object.
`__eq__`(other)	Return whether this IonChromatogram object is equal to another object.
`__len__`()	Returns the length of the IonChromatogram object.
`__sub__`(other)	Subtracts another IC from the current one (in place).
`dump`(file_name[, protocol])	Dumps an object to a file through `pickle.dump()`.
`get_index_at_time`(time)	Returns the nearest index corresponding to the given time.
`get_intensity_at_index`(ix)	Returns the intensity at the given index.
`get_time_at_index`(ix)	Returns time at given index.
`is_bpc`()	Returns whether the ion chromatogram is a base peak chromatogram (BPC).
`is_eic`()	Returns whether the ion chromatogram is an extracted ion chromatogram (EIC).
`is_tic`()	Returns whether the ion chromatogram is a total ion chromatogram (TIC) or extracted ion chromatogram (EIC).
`write`(file_name[, minutes, formatting])	Writes the ion chromatogram to the specified file.

Attributes:

`intensity_array`	Returns a copy of the intensity array.
`intensity_array_list`	Returns a copy of the intensity array as a list of lists of floats.
`intensity_matrix`	Returns a copy of the intensity matrix.
`mass`	Returns the m/z channel of the IC.
`masses`	List of extracted masses in the EIC.
`matrix_list`	Returns the intensity matrix as a list of lists of floats.
`time_list`	Returns a copy of the time list.
`time_step`	Returns the time step.

__copy__()

Returns a new IonChromatogram containing a copy of the data in this object.

Return type: IonChromatogram

__eq__(other)

Return whether this IonChromatogram object is equal to another object.

Parameters: other (Any) – The other object to test equality with.
Return type: bool

__len__()

Returns the length of the IonChromatogram object.

Authors: Lewis Lee, Vladimir Likic
Return type: int

__sub__(other)

Subtracts another IC from the current one (in place).

Parameters: other (IonChromatogram) – Another IC
Return type: IonChromatogram

dump(file_name, protocol=3)

Dumps an object to a file through pickle.dump().

Parameters

file_name (Union[str, Path, PathLike]) – Filename to save the dump as.
protocol (int) – The pickle protocol to use. Default 3.

Authors

Vladimir Likic, Dominic Davis-Foster (pathlib and pickle protocol support)

get_index_at_time(time)

Returns the nearest index corresponding to the given time.

Parameters: time (float) – Time in seconds
Return type: int
Returns: Nearest index corresponding to given time
Authors: Lewis Lee, Tim Erwin, Vladimir Likic

Changed in version 2.3.0: Now returns -1 if no index is found.

get_intensity_at_index(ix)

Returns the intensity at the given index.

Parameters: ix (int) – An index.
Authors: Lewis Lee, Vladimir Likic
Return type: float

get_time_at_index(ix)

Returns time at given index.

Parameters: ix (int)
Authors: Lewis Lee, Vladimir Likic
Return type: float

property intensity_array

Returns a copy of the intensity array.

Return type: ndarray
Returns: Matrix of intensity values.
Authors: Andrew Isaac, Lewis Lee

property intensity_array_list

Returns a copy of the intensity array as a list of lists of floats.

Return type: List[List[float]]
Returns: Matrix of intensity values.
Author: Andrew Isaac

property intensity_matrix

Returns a copy of the intensity matrix.

Return type: ndarray
Returns: Matrix of intensity values.
Author: Andrew Isaac

static is_bpc()

Returns whether the ion chromatogram is a base peak chromatogram (BPC).

New in version 2.3.0.

Return type: bool

static is_eic()[source]

Returns whether the ion chromatogram is an extracted ion chromatogram (EIC).

Return type: bool

is_tic()

Returns whether the ion chromatogram is a total ion chromatogram (TIC) or extracted ion chromatogram (EIC).

Authors: Lewis Lee, Vladimir Likic
Return type: bool

property mass

Returns the m/z channel of the IC.

Author: Sean O’Callaghan
Return type: Optional[float]

property masses

List of extracted masses in the EIC.

Return type: Tuple[float, …]

property matrix_list

Returns the intensity matrix as a list of lists of floats.

Return type: ndarray
Returns: Matrix of intensity values
Author: Andrew Isaac

property time_list

Returns a copy of the time list.

Return type: List[float]
Returns: List of retention times
Authors: Andrew Isaac, Lewis Lee, Vladimir Likic

property time_step

Returns the time step.

Authors: Lewis Lee, Vladimir Likic
Return type: float

write(file_name, minutes=False, formatting=True)

Writes the ion chromatogram to the specified file.

Parameters

file_name (Union[str, Path, PathLike]) – The name of the output file
minutes (bool) – A boolean value indicating whether to write time in minutes. Default False.
formatting (bool) – Whether to format the numbers in the output. Default True.

Authors

Lewis Lee, Vladimir Likic, Dominic Davis-Foster (pathlib support)

class IonChromatogram(intensity_list, time_list, mass=None)[source]

Bases: pymsBaseClass, TimeListMixin, IntensityArrayMixin, GetIndexTimeMixin

Models an ion chromatogram.

An ion chromatogram is a set of intensities as a function of retention time. This can can be either m/z channel intensities (for example, ion chromatograms at m/z = 65), or cumulative intensities over all measured m/z. In the latter case the ion chromatogram is total ion chromatogram (TIC).

The nature of an IonChromatogram object can be revealed by inspecting the value of the attribute ‘mass’. This is set to the m/z value of the ion chromatogram, or to None for TIC.

Parameters

intensity_list (Union[Sequence[float], ndarray]) – Ion chromatogram intensity values
time_list (Sequence[float]) – A list of ion chromatogram retention times
mass (Optional[float]) – Mass of ion chromatogram (None if TIC). Default None.

Authors

Lewis Lee, Vladimir Likic, Dominic Davis-Foster (type assertions and properties)

Changed in version 2.3.0: The ia parameter was renamed to intensity_list.

Methods:

`__copy__`()	Returns a new IonChromatogram containing a copy of the data in this object.
`__eq__`(other)	Return whether this IonChromatogram object is equal to another object.
`__len__`()	Returns the length of the IonChromatogram object.
`__sub__`(other)	Subtracts another IC from the current one (in place).
`dump`(file_name[, protocol])	Dumps an object to a file through `pickle.dump()`.
`get_index_at_time`(time)	Returns the nearest index corresponding to the given time.
`get_intensity_at_index`(ix)	Returns the intensity at the given index.
`get_time_at_index`(ix)	Returns time at given index.
`is_bpc`()	Returns whether the ion chromatogram is a base peak chromatogram (BPC).
`is_eic`()	Returns whether the ion chromatogram is an extracted ion chromatogram (EIC).
`is_tic`()	Returns whether the ion chromatogram is a total ion chromatogram (TIC) or extracted ion chromatogram (EIC).
`write`(file_name[, minutes, formatting])	Writes the ion chromatogram to the specified file.

Attributes:

`intensity_array`	Returns a copy of the intensity array.
`intensity_array_list`	Returns a copy of the intensity array as a list of lists of floats.
`intensity_matrix`	Returns a copy of the intensity matrix.
`mass`	Returns the m/z channel of the IC.
`matrix_list`	Returns the intensity matrix as a list of lists of floats.
`time_list`	Returns a copy of the time list.
`time_step`	Returns the time step.

__copy__()[source]

Returns a new IonChromatogram containing a copy of the data in this object.

Return type: IonChromatogram

__eq__(other)[source]

Return whether this IonChromatogram object is equal to another object.

Parameters: other (Any) – The other object to test equality with.
Return type: bool

__len__()[source]

Returns the length of the IonChromatogram object.

Authors: Lewis Lee, Vladimir Likic
Return type: int

__sub__(other)[source]

Subtracts another IC from the current one (in place).

Parameters: other (IonChromatogram) – Another IC
Return type: IonChromatogram

dump(file_name, protocol=3)

Dumps an object to a file through pickle.dump().

Parameters

file_name (Union[str, Path, PathLike]) – Filename to save the dump as.
protocol (int) – The pickle protocol to use. Default 3.

Authors

Vladimir Likic, Dominic Davis-Foster (pathlib and pickle protocol support)

get_index_at_time(time)

Returns the nearest index corresponding to the given time.

Parameters: time (float) – Time in seconds
Return type: int
Returns: Nearest index corresponding to given time
Authors: Lewis Lee, Tim Erwin, Vladimir Likic

Changed in version 2.3.0: Now returns -1 if no index is found.

get_intensity_at_index(ix)[source]

Returns the intensity at the given index.

Parameters: ix (int) – An index.
Authors: Lewis Lee, Vladimir Likic
Return type: float

get_time_at_index(ix)

Returns time at given index.

Parameters: ix (int)
Authors: Lewis Lee, Vladimir Likic
Return type: float

property intensity_array

Returns a copy of the intensity array.

Return type: ndarray
Returns: Matrix of intensity values.
Authors: Andrew Isaac, Lewis Lee

property intensity_array_list

Returns a copy of the intensity array as a list of lists of floats.

Return type: List[List[float]]
Returns: Matrix of intensity values.
Author: Andrew Isaac

property intensity_matrix

Returns a copy of the intensity matrix.

Return type: ndarray
Returns: Matrix of intensity values.
Author: Andrew Isaac

static is_bpc()[source]

Returns whether the ion chromatogram is a base peak chromatogram (BPC).

New in version 2.3.0.

Return type: bool

static is_eic()[source]

Returns whether the ion chromatogram is an extracted ion chromatogram (EIC).

New in version 2.3.0.

Return type: bool

is_tic()[source]

Returns whether the ion chromatogram is a total ion chromatogram (TIC) or extracted ion chromatogram (EIC).

Authors: Lewis Lee, Vladimir Likic
Return type: bool

property mass

Returns the m/z channel of the IC.

Author: Sean O’Callaghan
Return type: Optional[float]

property matrix_list

Returns the intensity matrix as a list of lists of floats.

Return type: ndarray
Returns: Matrix of intensity values
Author: Andrew Isaac

property time_list

Returns a copy of the time list.

Return type: List[float]
Returns: List of retention times
Authors: Andrew Isaac, Lewis Lee, Vladimir Likic

property time_step

Returns the time step.

Authors: Lewis Lee, Vladimir Likic
Return type: float

write(file_name, minutes=False, formatting=True)[source]

Writes the ion chromatogram to the specified file.

Parameters

file_name (Union[str, Path, PathLike]) – The name of the output file
minutes (bool) – A boolean value indicating whether to write time in minutes. Default False.
formatting (bool) – Whether to format the numbers in the output. Default True.

Authors

Lewis Lee, Vladimir Likic, Dominic Davis-Foster (pathlib support)

pyms.IonChromatogram

`pyms.IonChromatogram`