Mobilogram#

class pyopenms.Mobilogram(*args, **kwargs)#

Bases: Mobilogram

Mobilogram with DataFrame export capabilities.

This class extends Mobilogram with a get_df() method that converts mobilogram data to a pandas DataFrame.

__init__(*args, **kwargs)#

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: Mobilogram) → None

Methods

`__init__`(args, *kwargs)
`calculateTIC`(self)	Compute the total ion count (sum of all peak intensities)
`clear`(self)	Clears all data and ranges
`clearRanges`(self)	Resets all range dimensions as empty
`findNearest`(self, in_0)	Binary search for the peak nearest to a specific mobility :note: Make sure the mobilogram is sorted with respect to mobility! Otherwise the result is undefined
`getDriftTimeUnit`(self)	Returns the ion mobility drift time unit
`getDriftTimeUnitAsString`(self)	Returns the ion mobility drift time unit as string
`getFloatDataArrays`(self)	Returns a reference to the float meta data arrays
`getIntegerDataArrays`(self)	Returns a reference to the integer meta data arrays
`getMaxIntensity`(self)	Returns the maximum intensity
`getMaxMobility`(self)	Returns the maximum mobility
`getMinIntensity`(self)	Returns the minimum intensity
`getMinMobility`(self)	Returns the minimum mobility
`getRT`(self)	Returns the retention time (in seconds)
`getStringDataArrays`(self)	Returns a reference to the string meta data arrays
`get_data_dict`	Returns a dictionary of NumPy arrays with mobility, intensities, and metadata.
`get_df`([columns])	Returns a pandas DataFrame representation of the Mobilogram.
`get_df_columns`	Returns a list of column names that get_df() would produce for this mobilogram.
`get_peaks`
`isSorted`(self)	Checks if all peaks are sorted with respect to ascending mobility
`push_back`(self, in_0)	Append a peak
`reserve`(self, n)
`resize`(self, n)	Resize the peak array
`setDriftTimeUnit`(self, dt)	Sets the ion mobility drift time unit
`setFloatDataArrays`(self, fda)	Sets the float meta data arrays
`setIntegerDataArrays`(self, ida)	Sets the integer meta data arrays
`setRT`(self, in_0)	Sets the retention time (in seconds)
`setStringDataArrays`(self, sda)	Sets the string meta data arrays
`set_peaks`
`size`(self)	Returns the number of peaks in the mobilogram
`sortByIntensity`(self, reverse)	Lexicographically sorts the peaks by their intensity
`sortByPosition`(self)	Lexicographically sorts the peaks by their position (mobility)
`updateRanges`(self)

calculateTIC(self) → float#: Compute the total ion count (sum of all peak intensities)

clear(self) → None#

Clears all data and ranges

Will delete (clear) all peaks contained in the mobilogram

clearRanges(self) → None#: Resets all range dimensions as empty

findNearest(self, in_0: float) → int#

Binary search for the peak nearest to a specific mobility :note: Make sure the mobilogram is sorted with respect to mobility! Otherwise the result is undefined

Parameters:: mb – The searched for mobility value
Returns:: Returns the index of the peak.
Raises:: Exception: Precondition is thrown if the mobilogram is empty (not only in debug mode)

getDriftTimeUnit(self) → int#: Returns the ion mobility drift time unit

getDriftTimeUnitAsString(self) → bytes | str | String#: Returns the ion mobility drift time unit as string

getFloatDataArrays(self) → List[FloatDataArray]#: Returns a reference to the float meta data arrays

getIntegerDataArrays(self) → List[IntegerDataArray]#: Returns a reference to the integer meta data arrays

getMaxIntensity(self) → float#: Returns the maximum intensity

getMaxMobility(self) → float#: Returns the maximum mobility

getMinIntensity(self) → float#: Returns the minimum intensity

getMinMobility(self) → float#: Returns the minimum mobility

getRT(self) → float#: Returns the retention time (in seconds)

getStringDataArrays(self) → List[StringDataArray]#: Returns a reference to the string meta data arrays

get_data_dict()#

Returns a dictionary of NumPy arrays with mobility, intensities, and metadata.

This method extracts mobilogram data including peaks into a dictionary format suitable for conversion to a pandas DataFrame.

Args:

columns (list or None): List of column names to include. If None, includes: all default columns. Use get_df_columns() to see all available columns.

Returns:

dict: Dictionary with requested columns as keys and numpy arrays as values.

‘mobility’: numpy array of mobility values (float64)
‘intensity’: numpy array of intensity values (float32)
‘rt’: retention time (float64)
‘drift_time_unit’: drift time unit string

Example:

>>> data = mobilogram.get_data_dict()
>>> data = mobilogram.get_data_dict(columns=['mobility', 'intensity'])

get_df(columns: None | List[str] = None) → DataFrame#

Returns a pandas DataFrame representation of the Mobilogram.

This method converts the mobilogram data (peaks, metadata) into a pandas DataFrame format.

Note: Mobilogram does not support meta values (no MetaInfoInterface).

Args:

columns (list or None): List of column names to include. If None,: includes all default columns. Use get_df_columns() to discover available columns.

Returns:

pd.DataFrame: DataFrame with requested columns. Default columns include:

mobility: mobility values of peaks
intensity: intensity values of peaks
rt: retention time (replicated for each peak)
drift_time_unit: drift time unit string

Example:

>>> # Get all default columns
>>> df = mobilogram.get_df()

>>> # Discover available columns
>>> print(mobilogram.get_df_columns())

>>> # Get only specific columns (faster)
>>> df = mobilogram.get_df(columns=['mobility', 'intensity'])

get_df_columns()#

Returns a list of column names that get_df() would produce for this mobilogram.

Useful for discovering available columns before export.

Args:

columns (str): ‘default’ for standard columns, ‘all’ for all available: columns including non-default ones.

Returns:

list: List of column name strings.

Example:

>>> cols = mobilogram.get_df_columns()
['mobility', 'intensity', 'rt', 'drift_time_unit']

get_peaks()#

isSorted(self) → bool#: Checks if all peaks are sorted with respect to ascending mobility

push_back(self, in_0: MobilityPeak1D) → None#: Append a peak

reserve(self, n: int) → None#

resize(self, n: int) → None#: Resize the peak array

setDriftTimeUnit(self, dt: int) → None#: Sets the ion mobility drift time unit

setFloatDataArrays(self, fda: List[FloatDataArray]) → None#: Sets the float meta data arrays

setIntegerDataArrays(self, ida: List[IntegerDataArray]) → None#: Sets the integer meta data arrays

setRT(self, in_0: float) → None#: Sets the retention time (in seconds)

setStringDataArrays(self, sda: List[StringDataArray]) → None#: Sets the string meta data arrays

set_peaks()#

size(self) → int#: Returns the number of peaks in the mobilogram

sortByIntensity(self, reverse: bool) → None#

Lexicographically sorts the peaks by their intensity

Sorts the peaks according to ascending intensity. Meta data arrays will be sorted accordingly

sortByPosition(self) → None#

Lexicographically sorts the peaks by their position (mobility)

The mobilogram is sorted with respect to position (mobility). Meta data arrays will be sorted accordingly

updateRanges(self) → None#