Index

_

__add__() (esmraldi.sparsematrix.SparseMatrix method) __array_function__() (esmraldi.msimageimpl.MSImageImplementation method) (esmraldi.sparsematrix.SparseMatrix method) __array_ufunc__() (esmraldi.msimageimpl.MSImageImplementation method) (esmraldi.sparsematrix.SparseMatrix method) __div__() (esmraldi.sparsematrix.SparseMatrix method) __eq__() (esmraldi.msimageimpl.MSImageImplementation method) __exit__() (esmraldi.imzmlparsermmapped.ImzMLParserMMapped method) __floordiv__() (esmraldi.sparsematrix.SparseMatrix method) __ge__() (esmraldi.msimageimpl.MSImageImplementation method) __getitem__() (esmraldi.msimagebase.MSImageBase method) (esmraldi.msimagefly.MSImageOnTheFly method) (esmraldi.msimageimpl.MSImageImplementation method) (esmraldi.sparsematrix.SparseMatrix method) __gt__() (esmraldi.msimageimpl.MSImageImplementation method) __iadd__() (esmraldi.sparsematrix.SparseMatrix method)

__idiv__() (esmraldi.sparsematrix.SparseMatrix method) __ifloordiv__() (esmraldi.sparsematrix.SparseMatrix method) __imod__() (esmraldi.sparsematrix.SparseMatrix method) __imul__() (esmraldi.sparsematrix.SparseMatrix method) __ipow__() (esmraldi.sparsematrix.SparseMatrix method) __isub__() (esmraldi.sparsematrix.SparseMatrix method) __itruediv__() (esmraldi.sparsematrix.SparseMatrix method) __le__() (esmraldi.msimageimpl.MSImageImplementation method) __lt__() (esmraldi.msimageimpl.MSImageImplementation method) __mod__() (esmraldi.sparsematrix.SparseMatrix method) __mul__() (esmraldi.sparsematrix.SparseMatrix method) __ne__() (esmraldi.msimageimpl.MSImageImplementation method) __pow__() (esmraldi.sparsematrix.SparseMatrix method) __setitem__() (esmraldi.sparsematrix.SparseMatrix method) __sub__() (esmraldi.sparsematrix.SparseMatrix method) __truediv__() (esmraldi.sparsematrix.SparseMatrix method) _find_start_end() (in module esmraldi.sparsematrix)

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) align() (esmraldi.peakdetectionmeanspectrum.PeakDetectionMeanSpectrum method) annotation() (in module esmraldi.spectrainterpretation) annotation_ratio() (in module esmraldi.spectrainterpretation) apply_registration() (in module esmraldi.registration)

astype() (esmraldi.msimagebase.MSImageBase method) (esmraldi.msimagefly.MSImageOnTheFly method) (esmraldi.msimageimpl.MSImageImplementation method) attempt_reshape() (in module esmraldi.utils) auc_roc() (in module esmraldi.fusion) average_area() (in module esmraldi.segmentation) average_distance_graph() (in module esmraldi.segmentation) average_image() (esmraldi.msimageimpl.MSImageImplementation method)

B

best_fit() (in module esmraldi.registration) binary_closing() (in module esmraldi.segmentation) bisect_spectrum() (esmraldi.msimagefly.MSImageOnTheFly method)

broadcast_to() (esmraldi.sparsematrix.SparseMatrix method) build_h5() (in module esmraldi.imzlio_mmap) build_mmap() (in module esmraldi.imzlio_mmap) button_tooltip_on_hover() (in module esmraldi.utils)

C

center_images() (in module esmraldi.imageutils) chunk_process() (in module esmraldi.imzlio_mmap) 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) clustering_with_centers() (in module esmraldi.segmentation) compute_DT() (in module esmraldi.imageutils) compute_mean_spectra() (esmraldi.msimagebase.MSImageBase method) compute_projections() (esmraldi.fastmap.FastMap method) concatenate() (in module esmraldi.msimage) convolve2d() (in module esmraldi.haarpsi)

coords (esmraldi.msimageimpl.MSImageImplementation property) copy() (esmraldi.msimagebase.MSImageBase method) (esmraldi.msimagefly.MSImageOnTheFly method) (esmraldi.msimageimpl.MSImageImplementation method) cosine_neighborhood() (in module esmraldi.fusion) count_nonzero() (in module esmraldi.sparsematrix) create_group_hierarchy() (esmraldi.peakdetectiontree.PeakDetectionTree method) create_groups() (esmraldi.peakdetectiontree.PeakDetectionTree method) create_tree() (esmraldi.peakdetectiontree.PeakDetectionTree method) crop_image() (in module esmraldi.registration) cutoff_distance() (in module esmraldi.fusion) cutoff_distance2() (in module esmraldi.fusion) cutoff_efficiency() (in module esmraldi.fusion) cutoff_generalized_youden() (in module esmraldi.fusion) cutoff_half_tpr() (in module esmraldi.fusion)

D

data (esmraldi.msimageimpl.MSImageImplementation property) deisotoping_reference_indices() (in module esmraldi.spectraprocessing) deisotoping_simple() (in module esmraldi.spectraprocessing) deisotoping_simple_reference() (in module esmraldi.spectraprocessing) delete() (in module esmraldi.sparsematrix) detect_circle() (in module esmraldi.segmentation) detect_tube() (in module esmraldi.segmentation) determine_on_off_sample() (in module esmraldi.segmentation) determine_shape() (esmraldi.msimage.MSImage method)

display_all_slices() (esmraldi.viewer3D.Slicer method) dist2_minus_proj() (esmraldi.fastmap.FastMap method) distance_distribution() (in module esmraldi.segmentation) distance_point_to_set() (in module esmraldi.imageutils) distances_closest_neighbour() (in module esmraldi.segmentation) dt_mse() (in module esmraldi.imageutils) dt_mutual_information() (in module esmraldi.registration) dtype (esmraldi.msimagebase.MSImageBase property) (esmraldi.msimagefly.MSImageOnTheFly property) (esmraldi.msimageimpl.MSImageImplementation property)

E

enforce_continuity_values() (in module esmraldi.imageutils) esmraldi module esmraldi.fastmap module esmraldi.fusion module esmraldi.haarpsi module esmraldi.imageutils module esmraldi.imzlio_mmap module esmraldi.imzmlio module esmraldi.imzmlparsermmapped module esmraldi.msimage module esmraldi.msimagebase module esmraldi.msimagefly module esmraldi.msimageimpl module esmraldi.peakdetectionmeanspectrum module esmraldi.peakdetectiontree module esmraldi.registration module

esmraldi.segmentation module esmraldi.sliceviewer module esmraldi.sparsematrix module esmraldi.speciesrule module esmraldi.spectrainterpretation module esmraldi.spectralviewer module esmraldi.spectraprocessing module esmraldi.theoreticalspectrum module esmraldi.utils 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_mean_spectra_coordinates() (in module esmraldi.spectraprocessing) extract_peaks() (esmraldi.peakdetectionmeanspectrum.PeakDetectionMeanSpectrum method) (esmraldi.peakdetectiontree.PeakDetectionTree method) extract_peaks_from_distribution() (in module esmraldi.segmentation) extract_ratio_images() (in module esmraldi.fusion)

F

factors() (in module esmraldi.utils) FastMap (class in esmraldi.fastmap) fill_circle() (in module esmraldi.segmentation) fill_zeros_with_last() (esmraldi.peakdetectionmeanspectrum.PeakDetectionMeanSpectrum method) find_associated_distance_transforms() (in module esmraldi.segmentation) find_best_transformation() (in module esmraldi.registration) find_best_translation() (in module esmraldi.registration) find_best_translation_scale() (in module esmraldi.registration) find_isotopic_pattern() (in module esmraldi.spectraprocessing) find_isotopic_pattern_theoretical_difference() (in module esmraldi.spectraprocessing) find_levels_threshold() (esmraldi.peakdetectiontree.PeakDetectionTree method) find_peak_indices() (esmraldi.peakdetectionmeanspectrum.PeakDetectionMeanSpectrum method) find_peaks_group_hierarchy() (esmraldi.peakdetectiontree.PeakDetectionTree method) find_similar_image_distance_map_cc() (in module esmraldi.segmentation) find_similar_image_distance_map_percentile() (in module esmraldi.segmentation) find_similar_images_dispersion() (in module esmraldi.segmentation)

find_similar_images_dispersion_peaks() (in module esmraldi.segmentation) find_similar_images_distance_map() (in module esmraldi.segmentation) 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() (esmraldi.sparsematrix.SparseMatrix method) (in module esmraldi.fusion) fmeasure() (in module esmraldi.registration) fn_coordinates() (in module esmraldi.imzlio_mmap) fn_flatten() (in module esmraldi.imzlio_mmap) fn_image() (in module esmraldi.imzlio_mmap) fn_pixel_numbers() (in module esmraldi.imzlio_mmap) fn_unique() (in module esmraldi.imzlio_mmap) forward_derivatives() (in module esmraldi.spectraprocessing) furthest() (esmraldi.fastmap.FastMap method)

G

generate_random_distributions() (in module esmraldi.segmentation) geomeans() (in module esmraldi.utils) get_filename_h5() (in module esmraldi.imzlio_mmap) get_filename_mmap() (in module esmraldi.imzlio_mmap) get_full_spectra() (in module esmraldi.imzmlio) get_full_spectra_dense() (in module esmraldi.imzmlio) get_full_spectra_h5() (in module esmraldi.imzlio_mmap) get_full_spectra_mmap() (in module esmraldi.imzlio_mmap) get_full_spectra_sparse() (in module esmraldi.imzmlio) get_image() (in module esmraldi.imzmlio) get_images_from_spectra() (in module esmraldi.imzmlio) get_images_from_spectra_mmap() (in module esmraldi.imzlio_mmap) get_ion_image_index() (esmraldi.msimagebase.MSImageBase method) (esmraldi.msimagefly.MSImageOnTheFly method) (esmraldi.msimageimpl.MSImageImplementation method)

get_ion_image_mzs() (esmraldi.msimagebase.MSImageBase method) (esmraldi.msimagefly.MSImageOnTheFly method) (esmraldi.msimageimpl.MSImageImplementation method) get_nd_iterable_indices() (esmraldi.sparsematrix.SparseMatrix method) get_norm_image() (in module esmraldi.imageutils) 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_mmap() (in module esmraldi.imzlio_mmap) get_spectra_mzs() (in module esmraldi.imzmlio) get_spectra_reduced_mmap() (in module esmraldi.imzlio_mmap) get_spectrum_as_string() (esmraldi.imzmlparsermmapped.ImzMLParserMMapped method)

H

haar_psi() (in module esmraldi.haarpsi) haar_psi_numpy() (in module esmraldi.haarpsi)

haar_psi_tensorflow() (in module esmraldi.haarpsi) haar_wavelet_decompose() (in module esmraldi.haarpsi) heterogeneity_mask() (in module esmraldi.segmentation)

I

image_to_thresholded_variants() (in module esmraldi.fusion) ImzMLParserMMapped (class in esmraldi.imzmlparsermmapped) index_groups() (in module esmraldi.spectraprocessing) index_groups_start_end() (in module esmraldi.spectraprocessing) indices_search_sorted() (in module esmraldi.utils)

initialize_resampler() (in module esmraldi.registration) is_maybe_densify (esmraldi.msimageimpl.MSImageImplementation property) is_numpy() (in module esmraldi.haarpsi) is_tensorflow() (in module esmraldi.haarpsi) is_tensorflow_available (in module esmraldi.haarpsi) isotopes_from_pattern() (in module esmraldi.spectraprocessing)

J

json_to_species() (in module esmraldi.speciesrule)

L

load_h5() (in module esmraldi.imzlio_mmap) load_mmap() (in module esmraldi.imzlio_mmap) local_max_dt() (in module esmraldi.imageutils)

local_minima() (esmraldi.peakdetectiontree.PeakDetectionTree method) local_radius() (in module esmraldi.imageutils) logit() (in module esmraldi.haarpsi)

M

mapping_neighbors_average() (in module esmraldi.segmentation) max() (esmraldi.msimagebase.MSImageBase method) (esmraldi.msimagefly.MSImageOnTheFly method) (esmraldi.msimageimpl.MSImageImplementation method) max_area_slices() (in module esmraldi.imageutils) MAX_MAGNITUDE_ORDER (in module esmraldi.imzmlio) MAX_NUMBER (in module esmraldi.imzmlio) max_variance_sort() (in module esmraldi.segmentation) mean_spectra (esmraldi.msimagebase.MSImageBase property) measures_per_region() (in module esmraldi.fusion) median_minima() (in module esmraldi.segmentation) median_perimeter() (in module esmraldi.segmentation) merge_dicts_mz() (esmraldi.theoreticalspectrum.TheoreticalSpectrum method) min() (esmraldi.msimagebase.MSImageBase method) (esmraldi.msimagefly.MSImageOnTheFly method) (esmraldi.msimageimpl.MSImageImplementation method) min_step() (in module esmraldi.spectraprocessing) mix_molecules_regexp() (esmraldi.theoreticalspectrum.TheoreticalSpectrum method) mix_species() (esmraldi.theoreticalspectrum.TheoreticalSpectrum method) module esmraldi esmraldi.fastmap esmraldi.fusion esmraldi.haarpsi esmraldi.imageutils esmraldi.imzlio_mmap esmraldi.imzmlio esmraldi.imzmlparsermmapped esmraldi.msimage esmraldi.msimagebase esmraldi.msimagefly esmraldi.msimageimpl esmraldi.peakdetectionmeanspectrum esmraldi.peakdetectiontree esmraldi.registration esmraldi.segmentation esmraldi.sliceviewer esmraldi.sparsematrix esmraldi.speciesrule esmraldi.spectrainterpretation esmraldi.spectralviewer esmraldi.spectraprocessing esmraldi.theoreticalspectrum esmraldi.utils 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) MSImage (class in esmraldi.msimage) msimage_for_visualization() (in module esmraldi.utils) MSImageBase (class in esmraldi.msimagebase) MSImageImplementation (class in esmraldi.msimageimpl) MSImageOnTheFly (class in esmraldi.msimagefly) mutual_information() (in module esmraldi.registration) mz_second_isotope_most_abundant() (in module esmraldi.spectraprocessing)

N

ndim (esmraldi.msimagebase.MSImageBase property) (esmraldi.msimagefly.MSImageOnTheFly property) (esmraldi.msimageimpl.MSImageImplementation property) neighbours() (in module esmraldi.spectraprocessing) nmf() (in module esmraldi.fusion) nnz (esmraldi.msimageimpl.MSImageImplementation property) normalization_image (esmraldi.msimagebase.MSImageBase property)

normalization_sic() (in module esmraldi.spectraprocessing) normalization_tic() (in module esmraldi.spectraprocessing) normalize() (in module esmraldi.imzmlio) normalize_image() (in module esmraldi.imageutils) normalized_dt() (in module esmraldi.imageutils) not_indices() (esmraldi.peakdetectionmeanspectrum.PeakDetectionMeanSpectrum method) (esmraldi.peakdetectiontree.PeakDetectionTree method)

O

onclick() (esmraldi.spectralviewer.SpectralViewer method) onscroll() (esmraldi.sliceviewer.SliceViewer method)

open_imzml() (in module esmraldi.imzmlio) open_tif() (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) PeakDetectionMeanSpectrum (class in esmraldi.peakdetectionmeanspectrum) PeakDetectionTree (class in esmraldi.peakdetectiontree)

peaks (esmraldi.msimagebase.MSImageBase property) 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) preprocess_image() (in module esmraldi.registration) progress() (in module esmraldi.utils) properties_largest_area_cc() (in module esmraldi.segmentation) properties_median_perimeter() (in module esmraldi.segmentation) pseudo_flat_field_correction() (in module esmraldi.imageutils)

Q

quality_registration() (in module esmraldi.registration)

quantile_distance_distributions() (in module esmraldi.segmentation)

R

radius_maximal_balls() (in module esmraldi.imageutils) realign_generic() (in module esmraldi.spectraprocessing) realign_indices() (in module esmraldi.spectraprocessing) realign_mean_spectrum() (in module esmraldi.spectraprocessing) realign_mzs() (in module esmraldi.spectraprocessing) realign_reducing() (in module esmraldi.spectraprocessing) realign_tree() (in module esmraldi.spectraprocessing) realign_wrt_peaks() (in module esmraldi.spectraprocessing) realign_wrt_peaks_mzs() (in module esmraldi.spectraprocessing) realign_wrt_peaks_mzs_generic() (in module esmraldi.spectraprocessing) recall() (in module esmraldi.registration) reconstruct_image_from_components() (in module esmraldi.fusion) rectangle_coordinates() (in module esmraldi.imageutils) refresh() (esmraldi.viewer3D.Slicer method) region_growing() (in module esmraldi.segmentation) region_property_to_cc() (in module esmraldi.segmentation)

region_to_bool() (in module esmraldi.fusion) register() (in module esmraldi.registration) register_component_images() (in module esmraldi.registration) registration_landmarks() (in module esmraldi.registration) relative_area() (in module esmraldi.imageutils) remove_indices() (in module esmraldi.fusion) reshape() (esmraldi.msimagebase.MSImageBase method) (esmraldi.msimagefly.MSImageOnTheFly method) (esmraldi.msimageimpl.MSImageImplementation method) (esmraldi.sparsematrix.SparseMatrix method) resize() (in module esmraldi.imageutils) roc_auc_analysis() (in module esmraldi.fusion) roc_curve() (in module esmraldi.fusion) roc_curve_projection() (in module esmraldi.fusion) roc_cutoff_analysis() (in module esmraldi.fusion) roc_indices() (in module esmraldi.fusion)

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) shape (esmraldi.msimageimpl.MSImageImplementation property) sigmoid() (in module esmraldi.haarpsi) simple_vcm() (in module esmraldi.imageutils) single_measure() (in module esmraldi.fusion) single_roc_auc() (in module esmraldi.fusion) single_roc_cutoff() (in module esmraldi.fusion) size (esmraldi.msimagebase.MSImageBase property) (esmraldi.msimagefly.MSImageOnTheFly property) (esmraldi.msimageimpl.MSImageImplementation property) 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)

sparse_coordinates() (in module esmraldi.imzmlio) SparseMatrix (class in esmraldi.sparsematrix) spatial_chaos() (in module esmraldi.segmentation) spatial_coherence() (in module esmraldi.segmentation) spec (in module esmraldi.fastmap) species() (esmraldi.speciesrule.SpeciesRule method) SpeciesRule (class in esmraldi.speciesrule) spectra_max() (in module esmraldi.spectraprocessing) spectra_mean() (in module esmraldi.spectraprocessing) spectra_mean_centroided() (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) subsample() (in module esmraldi.haarpsi) subtract_spectra() (in module esmraldi.spectraprocessing)

T

take() (in module esmraldi.sparsematrix) TheoreticalSpectrum (class in esmraldi.theoreticalspectrum) tic (esmraldi.msimagebase.MSImageBase property) tic_values() (in module esmraldi.spectraprocessing) 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) to_tif() (in module esmraldi.imzmlio) tolerance() (in module esmraldi.utils) transpose() (esmraldi.msimagebase.MSImageBase method) (esmraldi.msimagefly.MSImageOnTheFly method) (esmraldi.msimageimpl.MSImageImplementation method) (esmraldi.sparsematrix.SparseMatrix method)

U

unique_mmap() (in module esmraldi.imzlio_mmap) update() (esmraldi.sliceviewer.SliceViewer method) (esmraldi.spectralviewer.SpectralViewer method) (esmraldi.viewer3D.Slicer method)

update_counts() (esmraldi.peakdetectiontree.PeakDetectionTree method) update_diffs() (esmraldi.peakdetectiontree.PeakDetectionTree method) update_hierarchy() (esmraldi.peakdetectiontree.PeakDetectionTree method)

V

variance_image() (in module esmraldi.imageutils) view() (esmraldi.msimagebase.MSImageBase method) (esmraldi.msimagefly.MSImageOnTheFly method) (esmraldi.msimageimpl.MSImageImplementation method) (esmraldi.sparsematrix.SparseMatrix method)

voronoi_diagram() (in module esmraldi.imageutils)

W

walklevel() (in module esmraldi.utils) weighted_distance() (in module esmraldi.fusion) weighted_roc_curve() (in module esmraldi.fusion)

width_peak_indices() (in module esmraldi.spectraprocessing) width_peak_mzs() (in module esmraldi.spectraprocessing) widths_peak_mass_resolution() (esmraldi.peakdetectionmeanspectrum.PeakDetectionMeanSpectrum method) write_imzml() (in module esmraldi.imzmlio)

Z

zeros() (in module esmraldi.sparsematrix)

zeros_like() (in module esmraldi.sparsematrix)