Welcome to native-fisher-py documentation

class native_fisher_py.InstrumentData[source]

Bases: CommonCoreDataObject

property axis_label_x

property axis_label_y

property channel_labels

clone()[source]

property flags

property hardware_version: str

property has_accurate_mass_precursors

property is_tsq_quantum_file

property is_valid

property model: str

property name: str

property serial_number: str

property software_version: str

property units

class native_fisher_py.RawFile(path: str)[source]

Bases: object

A high-level wrapper to provide a drop-in replacement for fisher_py.RawFile

property auto_sampler_information

average_scans(start, end)[source]

average_scans_in_scan_range(start, end, options)[source]

close()[source]

property computer_name: str

property creation_date: str

property creator_id: str

property default_mass_options

dispose()[source]

property file_error: FileError

static file_factory(path: str)[source]

property file_header: FileHeader

property file_name: str

property first_scan: int

get_all_instrument_names_from_instrument_method()[source]

get_auto_filters()[source]

get_average_ms2_scans_by_rt(rt_start, rt_end)[source]

get_averaged_ms2_scans(scan_numbers: List[int]) → Tuple[ndarray, ndarray, int][source]

get_centroid_stream(scan_number: int, include_ref_peaks: bool = False)[source]

get_chromatogram(mass: float = 0.0, tolerance: float = 0.0, trace_type: int = 1, ms_filter: str = 'ms') → Tuple[ndarray, ndarray][source]

get_chromatogram_data(settings, start_scan, end_scan, tolerance=None)[source]

get_error_log_item(index: int)[source]

get_filter_for_scan_number(scan_number)[source]

get_filters()[source]

get_instrument_count_of_type(device_type)[source]

get_instrument_data() → InstrumentData[source]

get_instrument_method(index)[source]

get_instrument_type()[source]

get_ms1_scan_number_from_retention_time(rt: float) → Tuple[int, float][source]

get_ms2_scan_number_from_retention_time(rt: float, precursor_mz: float = None) → Tuple[int, float][source]

get_precursor_mz(scan_number: int) → float[source]

get_retention_time_from_scan_number(scan_number: int) → float[source]

get_scan(scan_number: int)[source]

get_scan_dependents(scan_number, precision)[source]

get_scan_event_for_scan_number(scan_number: int)[source]

get_scan_event_str_from_scan_number(scan_number: int) → str[source]

get_scan_event_string_for_scan_number(scan_number: int)[source]

get_scan_events(start, end)[source]

get_scan_from_scan_number(scan_number: int)[source]

get_scan_ms1(scan_number: int)[source]

get_scan_ms2(*args)[source]

get_scan_number_from_retention_time(rt: float) → int[source]

get_scan_stats_for_scan_number(scan_number: int)[source]

get_scan_type(scan_number: int)[source]

get_segment_event_table()[source]

get_segmented_scan_from_scan_number(scan_number: int, stats=None)[source]

get_status_log_entries_count()[source]

get_status_log_for_retention_time(rt)[source]

get_status_log_for_scan_number(scan_number: int)[source]

get_status_log_header_information()[source]

get_status_log_values(scan_number, formatted=False)[source]

get_tic_ms2()[source]

get_trailer_extra_header_information()[source]

get_trailer_extra_information(scan_number)[source]

get_trailer_extra_values(scan_number, formatted=False)[source]

get_tune_data(index)[source]

get_tune_data_count()[source]

get_tune_data_header_information(index: int)[source]

get_tune_data_values(index: int)[source]

has_instrument_method()[source]

property has_ms_data: bool

property in_acquisition: bool

property include_reference_and_exception_data: bool

property instrument_count: int

property instrument_methods_count: int

property instrument_selection: InstrumentSelection

is_centroid_scan_from_scan_number(scan_number)[source]

property is_error: bool

property is_open: bool

property last_scan: int

property ms2_filter_masses: List[float]

property number_of_scans: int

property path: str

refresh_view_of_file()[source]

retention_time_from_scan_number(scan_number: int) → float[source]

property run_header: RunHeader

property run_header_ex: RunHeaderEx

property sample_information: SampleInformation

property scan_events: List[str]

scan_number_from_retention_time(rt: float) → int[source]

select_instrument(device_type: int, device_number: int)[source]

property selected_instrument

status_log_plottable_data()[source]

property total_time_min: float

property user_label: List[str]

exception native_fisher_py.RawFileException[source]: Bases: CoreException

class native_fisher_py.RunHeader(raw_file=None)[source]

Bases: CommonCoreDataObject

property end_time

property expected_runtime

property first_spectrum: int

property high_mass

property last_spectrum: int

property low_mass

property mass_resolution

property max_integrated_intensity

property max_intensity

property spectra_count

property start_time: float

property status_log_count

property tolerance_unit

property trailer_extra_count

property trailer_scan_event_count

property tune_data_count

class native_fisher_py.RunHeaderEx(raw_file)[source]

Bases: CommonCoreDataObject

property end_time

property error_message

property expected_runtime

property first_spectrum

property has_error

property has_warning

property high_mass

property last_spectrum

property low_mass

property mass_resolution

property max_integrated_intensity

property max_intensity

property spectra_count

property start_time

property trailer_extra_count

property warning_message

class native_fisher_py.SampleInformation[source]

Bases: CommonCoreDataObject

property barcode

property barcode_status

property calibration_file

property calibration_level

property comment

deep_copy()[source]

property dilution_factor

property injection_volume

property instrument_method_file

property istd_amount

property max_user_text_column_count

property path: str

property processing_method_file

property raw_file_name: str

property row_number

property sample_id

property sample_name

property sample_type

property sample_volume

property sample_weight

property user_text

property vial