Index

A

add_adduct_to_molecules() (esmraldi.theoreticalspectrum.TheoreticalSpectrum method) add_adducts_to_molecules_regexp() (esmraldi.theoreticalspectrum.TheoreticalSpectrum method) add_all_adducts_to_molecules() (esmraldi.theoreticalspectrum.TheoreticalSpectrum method)

annotation() (in module esmraldi.spectrainterpretation) annotation_ratio() (in module esmraldi.spectrainterpretation) average_area() (in module esmraldi.segmentation) average_distance_graph() (in module esmraldi.segmentation)

B

best_fit() (in module esmraldi.registration)

binary_closing() (in module esmraldi.segmentation)

C

center_images() (in module esmraldi.imageutils) closest_peak() (in module esmraldi.spectrainterpretation) (in module esmraldi.spectraprocessing) closest_pixels_cosine() (in module esmraldi.fusion) closest_reconstruction() (in module esmraldi.fusion)

clustering_affinity() (in module esmraldi.fusion) clustering_kmeans() (in module esmraldi.fusion) compute_DT() (in module esmraldi.imageutils) compute_projections() (esmraldi.fastmap.FastMap method) cosine_neighborhood() (in module esmraldi.fusion)

D

deisotoping_simple() (in module esmraldi.spectraprocessing) detect_circle() (in module esmraldi.segmentation) detect_tube() (in module esmraldi.segmentation) display_all_slices() (esmraldi.viewer3D.Slicer method)

dist2_minus_proj() (esmraldi.fastmap.FastMap method) distances_closest_neighbour() (in module esmraldi.segmentation) dt_mse() (in module esmraldi.imageutils) dt_mutual_information() (in module esmraldi.registration)

E

enforce_continuity_values() (in module esmraldi.imageutils) esmraldi module esmraldi.fastmap module esmraldi.fusion module esmraldi.imageutils module esmraldi.imzmlio module esmraldi.registration module esmraldi.segmentation module esmraldi.sliceviewer module

esmraldi.speciesrule module esmraldi.spectrainterpretation module esmraldi.spectralviewer module esmraldi.spectraprocessing module esmraldi.theoreticalspectrum module esmraldi.viewer3D module estimate_noise() (in module esmraldi.imageutils) estimate_plane() (in module esmraldi.imageutils) expand_mix() (esmraldi.theoreticalspectrum.TheoreticalSpectrum method) explaining_eigenvector() (in module esmraldi.fusion) export_figure_matplotlib() (in module esmraldi.imageutils) extract_ratio_images() (in module esmraldi.fusion)

F

FastMap (class in esmraldi.fastmap) fill_circle() (in module esmraldi.segmentation) find_best_transformation() (in module esmraldi.registration) find_best_translation() (in module esmraldi.registration) find_isotopic_pattern() (in module esmraldi.spectraprocessing) find_similar_images_spatial_chaos() (in module esmraldi.segmentation)

find_similar_images_spatial_coherence() (in module esmraldi.segmentation) find_similar_images_spatial_coherence_percentage() (in module esmraldi.segmentation) find_similar_images_variance() (in module esmraldi.segmentation) flatten() (in module esmraldi.fusion) fmeasure() (in module esmraldi.registration) forward_derivatives() (in module esmraldi.spectraprocessing) furthest() (esmraldi.fastmap.FastMap method)

G

get_full_spectra() (in module esmraldi.imzmlio) get_image() (in module esmraldi.imzmlio) get_images_from_spectra() (in module esmraldi.imzmlio) get_score() (in module esmraldi.fusion)

get_spectra() (in module esmraldi.imzmlio) get_spectra_from_images() (in module esmraldi.imzmlio) get_spectra_intensities() (in module esmraldi.imzmlio) get_spectra_mzs() (in module esmraldi.imzmlio)

I

index_groups() (in module esmraldi.spectraprocessing)

initialize_resampler() (in module esmraldi.registration) isotopes_from_pattern() (in module esmraldi.spectraprocessing)

J

json_to_species() (in module esmraldi.speciesrule)

L

local_max_dt() (in module esmraldi.imageutils)

local_radius() (in module esmraldi.imageutils)

M

max_area_slices() (in module esmraldi.imageutils) max_variance_sort() (in module esmraldi.segmentation) merge_dicts_mz() (esmraldi.theoreticalspectrum.TheoreticalSpectrum method) mix_molecules_regexp() (esmraldi.theoreticalspectrum.TheoreticalSpectrum method) mix_species() (esmraldi.theoreticalspectrum.TheoreticalSpectrum method) module esmraldi esmraldi.fastmap esmraldi.fusion esmraldi.imageutils esmraldi.imzmlio esmraldi.registration esmraldi.segmentation esmraldi.sliceviewer esmraldi.speciesrule esmraldi.spectrainterpretation esmraldi.spectralviewer esmraldi.spectraprocessing esmraldi.theoreticalspectrum esmraldi.viewer3D

molecules_regexp() (esmraldi.theoreticalspectrum.TheoreticalSpectrum method) mse() (in module esmraldi.imageutils) mse_numpy() (in module esmraldi.imageutils) mse_stddev() (in module esmraldi.imageutils) mutual_information() (in module esmraldi.registration) mz_second_isotope_most_abundant() (in module esmraldi.spectraprocessing)

N

neighbours() (in module esmraldi.spectraprocessing) nmf() (in module esmraldi.fusion) normalization_sic() (in module esmraldi.spectraprocessing)

normalization_tic() (in module esmraldi.spectraprocessing) normalize() (in module esmraldi.imzmlio) normalized_dt() (in module esmraldi.imageutils)

O

onclick() (esmraldi.spectralviewer.SpectralViewer method)

onscroll() (esmraldi.sliceviewer.SliceViewer method) open_imzml() (in module esmraldi.imzmlio)

P

parts_eval() (in module esmraldi.speciesrule) pca() (in module esmraldi.fusion) peak_indices() (in module esmraldi.spectraprocessing) peak_indices_cwt() (in module esmraldi.spectraprocessing) peak_reference_indices_group() (in module esmraldi.spectraprocessing) peak_reference_indices_groups() (in module esmraldi.spectraprocessing) peak_reference_indices_median() (in module esmraldi.spectraprocessing)

peak_to_index() (in module esmraldi.spectraprocessing) peaks_derivative_isotopic_pattern() (in module esmraldi.spectraprocessing) peaks_max_intensity_isotopic_pattern() (in module esmraldi.spectraprocessing) pick_pivots() (esmraldi.fastmap.FastMap method) post_processing() (in module esmraldi.fusion) precision() (in module esmraldi.registration) properties_largest_area_cc() (in module esmraldi.segmentation)

Q

quality_registration() (in module esmraldi.registration)

R

radius_maximal_balls() (in module esmraldi.imageutils) realign_indices() (in module esmraldi.spectraprocessing) realign_mzs() (in module esmraldi.spectraprocessing) realign_wrt_peaks() (in module esmraldi.spectraprocessing) realign_wrt_peaks_mzs() (in module esmraldi.spectraprocessing) recall() (in module esmraldi.registration) reconstruct_image_from_components() (in module esmraldi.fusion)

refresh() (esmraldi.viewer3D.Slicer method) region_growing() (in module esmraldi.segmentation) region_property_to_cc() (in module esmraldi.segmentation) register() (in module esmraldi.registration) register_component_images() (in module esmraldi.registration) relative_area() (in module esmraldi.imageutils) remove_indices() (in module esmraldi.fusion) resize() (in module esmraldi.imageutils)

S

same_mz_axis() (in module esmraldi.spectraprocessing) select_class_area() (in module esmraldi.segmentation) select_class_max_value() (in module esmraldi.segmentation) select_images() (in module esmraldi.fusion) setOTF() (esmraldi.viewer3D.Slicer method) simple_vcm() (in module esmraldi.imageutils) slice_correspondences() (in module esmraldi.imageutils) slice_correspondences_manual() (in module esmraldi.imageutils) Slicer (class in esmraldi.viewer3D) SliceViewer (class in esmraldi.sliceviewer) sliderOpacityThreshold() (esmraldi.viewer3D.Slicer method) sliderThreshold() (esmraldi.viewer3D.Slicer method) sort_size_ascending() (in module esmraldi.segmentation) spatial_chaos() (in module esmraldi.segmentation)

spatial_coherence() (in module esmraldi.segmentation) species() (esmraldi.speciesrule.SpeciesRule method) SpeciesRule (class in esmraldi.speciesrule) spectra_max() (in module esmraldi.spectraprocessing) spectra_mean() (in module esmraldi.spectraprocessing) spectra_min() (in module esmraldi.spectraprocessing) spectra_peak_indices() (in module esmraldi.spectraprocessing) spectra_peak_indices_adaptative() (in module esmraldi.spectraprocessing) spectra_peak_indices_adaptative_noiselevel() (in module esmraldi.spectraprocessing) spectra_peak_mzs_adaptative() (in module esmraldi.spectraprocessing) spectra_peak_mzs_adaptative_noiselevel() (in module esmraldi.spectraprocessing) spectra_peak_mzs_cwt() (in module esmraldi.spectraprocessing) spectra_sum() (in module esmraldi.spectraprocessing) SpectralViewer (class in esmraldi.spectralviewer) stddev_image() (in module esmraldi.imageutils)

T

TheoreticalSpectrum (class in esmraldi.theoreticalspectrum) to_csv() (in module esmraldi.imzmlio)

to_image_array() (in module esmraldi.imzmlio) to_image_array_3D() (in module esmraldi.imzmlio) to_nifti() (in module esmraldi.imzmlio)

U

update() (esmraldi.sliceviewer.SliceViewer method) (esmraldi.spectralviewer.SpectralViewer method) (esmraldi.viewer3D.Slicer method)

V

variance_image() (in module esmraldi.imageutils)

voronoi_diagram() (in module esmraldi.imageutils)

W

weighted_distance() (in module esmraldi.fusion) width_peak_indices() (in module esmraldi.spectraprocessing)

width_peak_mzs() (in module esmraldi.spectraprocessing) write_imzml() (in module esmraldi.imzmlio)