opentof 0.1.0__py3-none-any.whl

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Files changed (18) hide show
  1. opentof/__init__.py +171 -0
  2. opentof/compound_list.parquet +0 -0
  3. opentof/deployment.py +5051 -0
  4. opentof/interactive.py +812 -0
  5. opentof/isotopes.py +649 -0
  6. opentof/mass_calibration.py +2699 -0
  7. opentof/peak_fitting.py +2652 -0
  8. opentof/peak_width_shape.py +981 -0
  9. opentof/quantification.py +863 -0
  10. opentof/runner.py +243 -0
  11. opentof/som_helpers.py +638 -0
  12. opentof/utils.py +2339 -0
  13. opentof-0.1.0.dist-info/METADATA +264 -0
  14. opentof-0.1.0.dist-info/RECORD +18 -0
  15. opentof-0.1.0.dist-info/WHEEL +5 -0
  16. opentof-0.1.0.dist-info/entry_points.txt +2 -0
  17. opentof-0.1.0.dist-info/licenses/LICENSE +176 -0
  18. opentof-0.1.0.dist-info/top_level.txt +1 -0
opentof/__init__.py ADDED
@@ -0,0 +1,171 @@
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+ # Copyright 2026 Aerodyne Research, Inc.
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+ #
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+ # Licensed under the Apache License, Version 2.0 (the "License");
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+ # you may not use this file except in compliance with the License.
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+ # You may obtain a copy of the License at
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+ #
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+ # http://www.apache.org/licenses/LICENSE-2.0
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+ #
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+ # Unless required by applicable law or agreed to in writing, software
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+ # distributed under the License is distributed on an "AS IS" BASIS,
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+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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+ # See the License for the specific language governing permissions and
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+ # limitations under the License.
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+
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+ # opentof/__init__.py
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+ from opentof.deployment import Deployment
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+
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+ from opentof.runner import run_do_it, main
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+
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+ from opentof.mass_calibration import (
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+ generate_averaged_dataset,
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+ run_mass_calibration,
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+ define_reference_spectrum,
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+ combined_mc_aux_plots,
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+ mass_dependent_error_plot,
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+ estimate_global_noise_level,
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+ determine_baseline,
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+ apply_mass_calibration,
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+ fit_mass_calibration,
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+ MASS_CAL_MODES,
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+ get_mass_axis_for_ms_i,
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+ calibrate_mass,
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+ low_pass_filter,
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+ )
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+
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+ from opentof.peak_width_shape import (
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+ peak_width, peak_shape, ransac_peak_width,
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+ )
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+
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+ from opentof.peak_fitting import (
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+ gaussian, lorentzian, pseudo_voigt,
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+ peak_function_selector,
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+ fit_and_extract_pos,
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+ fit_single_peak,
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+ fit_mopf_nm,
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+ unpack_fit_result,
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+ generate_peak_mask,
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+ estimate_local_noise_level,
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+ multi_overlap_peak_fit,
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+ levenberg_marquardt,
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+ fit_unconstrained_peaks,
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+ full_fitting_integration_unconstrained,
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+ full_fitting_integration_constrained,
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+ fit_partially_constrained_nm,
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+ )
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+
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+ from opentof.isotopes import (
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+ convolve_distributions,
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+ element_distribution,
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+ calculate_isotope_masses,
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+ batch_isotope_masses,
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+ isotope_signal_on_axis,
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+ subtract_isotopes,
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+ reconstruct_total_isotope_signal,
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+ )
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+
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+ from opentof.utils import (
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+ return_mass, get_raw_nm_data, get_nm_segment_data,
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+ std_list_array_lengths,
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+ GlobalMinMaxScaler, ptoe,
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+ plot_peak_fits,
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+ plot_apd_peaks,
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+ print_h5_structure,
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+ median_absolute_deviation,
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+ calculate_rolling_average,
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+ activity_classifier,
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+ truncate,
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+ spectra_nm_split,
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+ aggregate_tw_expicit_time_export,
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+ regr_model_metrics,
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+ regr_scatter_plot,
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+ load_peak_list,
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+ ensure_dir,
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+ find_possible_compositions,
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+ cluster_discovered_peaks,
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+ get_default_plot_dir,
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+ )
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+
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+ from opentof.quantification import (
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+ load_TWEB_sensitivity_calibration_file,
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+ quantify_signal,
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+ )
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+
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+ # Experimental
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+ from opentof.som_helpers import (
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+ RowMinMaxScaler, build_nm_som, organize_som_data,
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+ process_som_weight_peaks,
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+ )
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+
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+ __all__ = [
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+ "Deployment",
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+ "run_do_it",
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+ "main",
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+ "return_mass",
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+ "get_raw_nm_data",
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+ "get_nm_segment_data",
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+ "std_list_array_lengths",
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+ "GlobalMinMaxScaler",
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+ "ptoe",
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+ "plot_peak_fits",
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+ "plot_apd_peaks",
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+ "print_h5_structure",
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+ "median_absolute_deviation",
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+ "calculate_rolling_average",
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+ "activity_classifier",
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+ "truncate",
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+ "spectra_nm_split",
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+ "aggregate_tw_expicit_time_export",
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+ "regr_model_metrics",
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+ "regr_scatter_plot",
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+ "load_peak_list",
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+ "generate_averaged_dataset",
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+ "run_mass_calibration",
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+ "define_reference_spectrum",
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+ "combined_mc_aux_plots",
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+ "mass_dependent_error_plot",
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+ "estimate_global_noise_level",
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+ "determine_baseline",
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+ "apply_mass_calibration",
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+ "fit_mass_calibration",
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+ "MASS_CAL_MODES",
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+ "get_mass_axis_for_ms_i",
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+ "calibrate_mass",
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+ "low_pass_filter",
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+ "gaussian",
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+ "lorentzian",
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+ "pseudo_voigt",
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+ "peak_function_selector",
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+ "fit_and_extract_pos",
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+ "fit_single_peak",
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+ "fit_mopf_nm",
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+ "unpack_fit_result",
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+ "generate_peak_mask",
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+ "estimate_local_noise_level",
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+ "multi_overlap_peak_fit",
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+ "levenberg_marquardt",
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+ "full_fitting_integration_unconstrained",
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+ "fit_unconstrained_peaks",
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+ "full_fitting_integration_constrained",
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+ "fit_partially_constrained_nm",
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+ "peak_width",
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+ "ransac_peak_width",
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+ "peak_shape",
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+ "RowMinMaxScaler",
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+ "build_nm_som",
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+ "organize_som_data",
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+ "process_som_weight_peaks",
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+ "load_TWEB_sensitivity_calibration_file",
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+ "quantify_signal",
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+ "ensure_dir",
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+ "find_possible_compositions",
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+ "cluster_discovered_peaks",
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+ "get_default_plot_dir",
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+ "convolve_distributions",
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+ "element_distribution",
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+ "calculate_isotope_masses",
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+ "batch_isotope_masses",
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+ "isotope_signal_on_axis",
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+ "subtract_isotopes",
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+ "reconstruct_total_isotope_signal",
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+ ]
opentof/compound_list.parquet ADDED
Binary file