Index

A

abscorr2() (in module XRStools.xrs_utilities), [1] absCorrection() (in module XRStools.xrs_utilities), [1] absolute_cross_section (class in XRStools.xrs_prediction) absorptionCorrectProfiles() (XRStools.xrs_ComptonProfiles.AtomProfile method) add_scan() (XRStools.xrs_scans.Scan method) addch() (in module XRStools.xrs_utilities), [1] alignment_image() (in module XRStools.xrs_read) alignment_image_new() (in module XRStools.xrs_read) alignment_image_old() (in module XRStools.xrs_read) alignRCmonitor() (XRStools.xrs_scans.offDiaDataSet method) alignRCmonitor2() (XRStools.xrs_scans.offDiaDataSet method) alignRCmonitorCC() (XRStools.xrs_scans.offDiaDataSet method) alterGROatomNames() (in module XRStools.xrs_calctools) analyzer (class in XRStools.xrs_prediction) analyzerAverage() (XRStools.xrs_extraction.edge_extraction method) animation() (in module XRStools.xrs_read)

append() (XRStools.xrs_rois.roi_object method) append2Scan_left() (in module XRStools.xrs_scans) append2Scan_right() (in module XRStools.xrs_scans) append_scan() (XRStools.xrs_scans.Scan method) appendAtom() (XRStools.xrs_calctools.xyzMolecule method) appendROIobject() (XRStools.roifinder_and_gui.roi_finder method) appendScans() (in module XRStools.xrs_scans) appendScans_pixel() (in module XRStools.xrs_scans) appendXESScans() (in module XRStools.xrs_scans) apply_rois() (XRStools.xrs_scans.Scan method) apply_rois_pw() (XRStools.xrs_scans.Scan method) applyrois() (XRStools.xrs_scans.scan method) applyrois_pw() (XRStools.xrs_scans.scan method) assign() (XRStools.xrs_scans.Scan method) AtomProfile (class in XRStools.xrs_ComptonProfiles) axsfTrajParser() (in module XRStools.xrs_calctools)

B

beam (class in XRStools.xrs_prediction) bidiag_reduction() (in module XRStools.xrs_utilities), [1] bootstrapCNNMF() (in module XRStools.xrs_utilities), [1] bootstrapCNNMF_old() (in module XRStools.xrs_utilities), [1] boxParser() (in module XRStools.xrs_calctools) bragg() (in module XRStools.xrs_utilities), [1]

bragg_refl (class in XRStools.xrs_utilities), [1] braggd() (in module XRStools.xrs_utilities), [1] break_down_det_image() (in module XRStools.xrs_rois) broaden_diagram() (in module XRStools.xrs_calctools) broaden_lin() (XRStools.xrs_calctools.erkale method) (XRStools.xrs_calctools.stobe method) broaden_linear() (in module XRStools.xrs_calctools)

C

calc_abs_cross_section() (XRStools.xrs_prediction.absolute_cross_section method) calc_HF_profiles() (XRStools.xrs_prediction.compton_profiles method) calc_num_scatterers() (XRStools.xrs_prediction.absolute_cross_section method) calc_pure_HF_profiles() (XRStools.xrs_prediction.compton_profiles method) calculateCOMlist() (in module XRStools.xrs_calctools) calculateRIJhist() (in module XRStools.xrs_calctools) calculateRIJhist2_arb() (in module XRStools.xrs_calctools) calculateRIJhist_arb() (in module XRStools.xrs_calctools) catScans() (in module XRStools.xrs_scans) catScans_pixel() (in module XRStools.xrs_scans) catScansLong() (in module XRStools.xrs_scans) catXESScans() (in module XRStools.xrs_scans) changeOHBondLength() (in module XRStools.xrs_calctools) changeOHBondlength() (XRStools.xrs_calctools.xyzBox method) Chi() (in module XRStools.xrs_utilities), [1] cixs_primo() (in module XRStools.xrs_utilities), [1] cixs_secondo() (in module XRStools.xrs_utilities), [1] cixs_terzo() (in module XRStools.xrs_utilities), [1] cixsUBfind() (in module XRStools.xrs_utilities), [1] cixsUBgetAngles_primo() (in module XRStools.xrs_utilities), [1] cixsUBgetAngles_secondo() (in module XRStools.xrs_utilities), [1] cixsUBgetAngles_terzo() (in module XRStools.xrs_utilities), [1] cixsUBgetQ_primo() (in module XRStools.xrs_utilities), [1] cixsUBgetQ_secondo() (in module XRStools.xrs_utilities), [1] cixsUBgetQ_terzo() (in module XRStools.xrs_utilities), [1] cla() (in module XRStools.xrs_prediction) cNNMF_chris() (in module XRStools.xrs_utilities), [1] compton_profiles (class in XRStools.xrs_prediction) ComptonProfiles (class in XRStools.xrs_ComptonProfiles) compute() (XRStools.xrs_prediction.matrix_element method) compute_matrix_elements() (in module XRStools.xrs_utilities), [1] con2mat() (in module XRStools.xrs_utilities), [1] constrained_mf() (in module XRStools.xrs_utilities), [1] constrained_svd() (in module XRStools.xrs_utilities), [1]

container (class in XRStools.xrs_rois) convert_inds_to_matrix() (in module XRStools.xrs_rois) convert_inds_to_xinds() (in module XRStools.xrs_rois) convert_inds_to_yinds() (in module XRStools.xrs_rois) convert_matrix_rois_to_inds() (in module XRStools.xrs_rois) convert_matrix_to_redmatrix() (in module XRStools.xrs_rois) convert_redmatrix_to_matrix() (in module XRStools.xrs_rois) convert_redmatrix_to_matrix_my() (in module XRStools.xrs_rois) convert_roi_matrix_to_masks() (in module XRStools.xrs_rois) convertSplitEDF2EDF() (in module XRStools.xrs_utilities), [1] convg() (in module XRStools.xrs_calctools) (in module XRStools.xrs_utilities), [1] convtoprim() (in module XRStools.xrs_utilities), [1] copy_edf_files() (XRStools.xrs_read.Fourc method) (XRStools.xrs_read.Hydra method) (XRStools.xrs_read.read_id20 method) count_contact_pairs() (XRStools.xrs_calctools.xyzBox method) count_hbonds() (XRStools.xrs_calctools.xyzBox method) count_HBonds_pbc_arb() (in module XRStools.xrs_calctools) count_neighbors() (XRStools.xrs_calctools.xyzBox method) count_OO_neighbors() (in module XRStools.xrs_calctools) count_OO_neighbors_pbc() (in module XRStools.xrs_calctools) countHbonds() (in module XRStools.xrs_calctools) countHbonds_orig() (in module XRStools.xrs_calctools) countHbonds_pbc() (in module XRStools.xrs_calctools) create_diff_image() (in module XRStools.roifinder_and_gui) (in module XRStools.xrs_scans) create_rois() (in module XRS_swissknife) create_sum_image() (in module XRStools.xrs_scans) cshift() (in module XRStools.xrs_utilities), [1] cut_broadspecs() (XRStools.xrs_calctools.erkale method) cut_rawspecs() (XRStools.xrs_calctools.erkale method) (XRStools.xrs_calctools.stobe method) cut_spec() (in module XRStools.xrs_calctools)

D

define_lin_roi() (in module XRStools.roifinder_and_gui) define_polygon_roi() (in module XRStools.roifinder_and_gui) define_zoom_roi() (in module XRStools.roifinder_and_gui) deglitchSignalMatrix() (XRStools.xrs_scans.offDiaDataSet method) delE_dicedAnalyzerIntrinsic() (in module XRStools.xrs_utilities), [1] delE_JohannAberration() (in module XRStools.xrs_utilities), [1] delE_offRowland() (in module XRStools.xrs_utilities), [1] delE_pixelSize() (in module XRStools.xrs_utilities), [1] delE_sourceSize() (in module XRStools.xrs_utilities), [1] delE_stressedCrystal() (in module XRStools.xrs_utilities), [1] delete_empty_rois() (XRStools.xrs_rois.roi_object method) delete_scan() (XRStools.xrs_read.Fourc method) (XRStools.xrs_read.Hydra method) deleterois() (XRStools.roifinder_and_gui.roi_finder method)

deletescan() (XRStools.xrs_read.read_id20 method) deleteTip4pCOM() (XRStools.xrs_calctools.xyzBox method) detector (class in XRStools.xrs_prediction) diode() (in module XRStools.xrs_utilities), [1] dspace() (in module XRStools.xrs_utilities), [1] dtxrd (class in XRStools.xrs_utilities), [1] dtxrd_anomalous_absorption() (in module XRStools.xrs_utilities), [1] dtxrd_extinction_length() (in module XRStools.xrs_utilities), [1] dtxrd_reflectivity() (in module XRStools.xrs_utilities), [1] dump_on_file_list() (in module XRStools.xrs_fileIO) dump_scans_ascii() (XRStools.xrs_read.Fourc method) (XRStools.xrs_read.Hydra method) dump_spectrum_ascii() (XRStools.xrs_read.Hydra method) dump_spectrum_hdf5() (XRStools.xrs_read.Hydra method)

E

e2pz() (in module XRStools.xrs_utilities), [1] edf_cleaner() (in module XRStools.xrs_scans) EdfRead() (in module XRStools.xrs_fileIO) edfread() (in module XRStools.xrs_utilities), [1] edfread_test() (in module XRStools.xrs_utilities), [1] edge_extraction (class in XRStools.xrs_extraction) element() (in module XRStools.xrs_utilities), [1] elossProfile() (in module XRStools.xrs_ComptonProfiles)

energy() (in module XRStools.xrs_utilities), [1] energy_monoangle() (in module XRStools.xrs_utilities), [1] erkale (class in XRStools.xrs_calctools) estimate_shift() (in module XRStools.xrs_imaging) estimate_shifts() (XRStools.xrs_imaging.imageset method) estimate_xshift() (in module XRStools.xrs_imaging) estimate_xshifts() (XRStools.xrs_imaging.imageset method) estimate_yshift() (in module XRStools.xrs_imaging) estimate_yshifts() (XRStools.xrs_imaging.imageset method)

F

FabioEdfRead() (in module XRStools.xrs_fileIO) fermi() (in module XRStools.xrs_utilities), [1] filterDetErrors() (XRStools.xrs_scans.offDiaDataSet method) find_center_of_mass() (in module XRStools.xrs_utilities), [1] find_cw_rois() (XRStools.roifinder_and_gui.roi_finder method) find_diag_angles() (in module XRStools.xrs_utilities), [1] find_H2O_molecules() (in module XRStools.xrs_calctools) find_H2O_molecules_PBC_arb() (in module XRStools.xrs_calctools) find_hydroniums() (XRStools.xrs_calctools.xyzBox method) find_hydroxides() (XRStools.xrs_calctools.xyzBox method) find_pw_rois() (XRStools.roifinder_and_gui.roi_finder method) find_tmao_molecules_arb() (XRStools.xrs_calctools.xyzBox method) find_urea_molecules_arb() (XRStools.xrs_calctools.xyzBox method)

findAllWaters() (in module XRStools.xrs_calctools) findgroups() (in module XRStools.xrs_scans) findHexaneMolecules() (in module XRStools.xrs_calctools) findMethAndHexMolecules() (XRStools.xrs_calctools.xyzBox method) findMethanolMolecules() (in module XRStools.xrs_calctools) (XRStools.xrs_calctools.xyzBox method) findMolecule() (in module XRStools.xrs_calctools) findScans_bytype() (in module XRStools.xrs_scans) FormulaProfile (class in XRStools.xrs_ComptonProfiles) Fourc (class in XRStools.xrs_read) funct() (XRStools.xrs_extraction.functorObjectV method) functorObjectV (class in XRStools.xrs_extraction) fwhm() (in module XRStools.xrs_utilities), [1]

G

gauss() (in module XRStools.xrs_calctools) (in module XRStools.xrs_utilities), [1] gauss1() (in module XRStools.xrs_calctools) gauss_areanorm() (in module XRStools.xrs_calctools) generality_doc (in module XRS_swissknife) get_absorption_correction() (XRStools.xrs_prediction.sample method) get_all_input() (in module XRStools.xrs_prediction) get_alpha() (XRStools.xrs_prediction.sample method) get_angle() (XRStools.xrs_calctools.xyzBox method) get_angle_arb() (XRStools.xrs_calctools.xyzBox method) get_anomalous_absorption() (XRStools.xrs_utilities.dtxrd method), [1] get_asymmetry() (XRStools.xrs_extraction.valence_CP method) get_atoms_by_name() (XRStools.xrs_calctools.xyzBox method) (XRStools.xrs_calctools.xyzMolecule method) get_atoms_from_molecules() (XRStools.xrs_calctools.xyzBox method) get_auto_rois() (XRStools.roifinder_and_gui.roi_finder method) get_auto_rois_eachdet() (XRStools.roifinder_and_gui.roi_finder method) get_average_densities() (XRStools.xrs_prediction.sample method) get_beam_cross_section_area() (XRStools.xrs_prediction.beam method) get_beam_height() (XRStools.xrs_prediction.beam method) get_beam_height_cm() (XRStools.xrs_prediction.beam method) get_beam_width() (XRStools.xrs_prediction.beam method) get_beam_width_cm() (XRStools.xrs_prediction.beam method) get_bend_r() (XRStools.xrs_prediction.analyzer method) get_beta() (XRStools.xrs_prediction.sample method) get_bounding_boxes() (XRStools.xrs_rois.roi_object method) get_C_edges_av() (XRStools.xrs_extraction.HF_dataset method) get_C_total() (XRStools.xrs_extraction.HF_dataset method) get_chi() (XRStools.xrs_utilities.bragg_refl method), [1] get_compensation_factor() (XRStools.xrs_read.Fourc method) (XRStools.xrs_read.Hydra method) (XRStools.xrs_read.Hydra_imaging method) get_concentrations() (XRStools.xrs_prediction.sample method) get_copy() (XRStools.xrs_rois.roi_object method) get_correctecProfiles() (XRStools.xrs_ComptonProfiles.FormulaProfile method) get_data() (XRStools.xrs_read.Fourc method) (XRStools.xrs_read.Hydra method) get_data_new() (XRStools.xrs_read.Hydra method) get_data_pw() (XRStools.xrs_read.Hydra method) get_densities() (XRStools.xrs_prediction.sample method) get_det_name() (XRStools.xrs_utilities.maxipix_det method), [1] get_diced() (XRStools.xrs_prediction.analyzer method) get_divergence() (XRStools.xrs_prediction.beam method) get_E0() (XRStools.xrs_prediction.compton_profiles method) get_E_end() (XRStools.xrs_scans.Scan method) get_E_start() (XRStools.xrs_scans.Scan method) get_eend() (XRStools.xrs_scans.Scan_group method) (XRStools.xrs_scans.scangroup method) get_efficiency() (XRStools.xrs_prediction.analyzer method) (XRStools.xrs_prediction.detector method) get_Ein_RIXS_map() (XRStools.xrs_read.Fourc method) get_eloss() (XRStools.xrs_read.Hydra method) get_eloss_new() (XRStools.xrs_read.Hydra method) get_eloss_pw() (XRStools.xrs_scans.scan method) get_elossProfiles() (XRStools.xrs_ComptonProfiles.AtomProfile method) (XRStools.xrs_ComptonProfiles.FormulaProfile method) (XRStools.xrs_ComptonProfiles.HFProfile method) get_energy() (XRStools.xrs_prediction.detector method) get_energy1() (XRStools.xrs_prediction.sample method) get_energy2() (XRStools.xrs_prediction.sample method) get_energy_in_keV() (XRStools.xrs_prediction.compton_profiles method) get_energy_resolution() (XRStools.xrs_prediction.analyzer method) get_energy_resolution_keV() (XRStools.xrs_prediction.analyzer method) get_estart() (XRStools.xrs_scans.Scan_group method) (XRStools.xrs_scans.scangroup method) get_eta() (XRStools.xrs_utilities.dtxrd method), [1] get_extinction_length() (XRStools.xrs_utilities.dtxrd method), [1] get_formulas() (XRStools.xrs_prediction.sample method) get_geo_informations() (in module XRStools.xrs_rois) get_gnuplot_rgb() (in module XRStools.xrs_utilities), [1] get_h2o_molecules() (XRStools.xrs_calctools.xyzBox method) get_h2o_molecules_arb() (XRStools.xrs_calctools.xyzBox method) get_hbonds() (XRStools.xrs_calctools.xyzBox method) get_HF_profiles() (XRStools.xrs_prediction.compton_profiles method) get_hkl() (XRStools.xrs_prediction.analyzer method) get_i0_intensity() (XRStools.xrs_prediction.beam method) get_indices() (XRStools.xrs_rois.roi_object method) get_J_total_av() (XRStools.xrs_extraction.HF_dataset method) get_linear_rois() (XRStools.roifinder_and_gui.roi_finder method) get_mask_d() (XRStools.xrs_prediction.analyzer method) get_masks() (XRStools.xrs_rois.roi_object method) get_material() (XRStools.xrs_prediction.analyzer method) (XRStools.xrs_prediction.detector method) get_maxediff() (XRStools.xrs_scans.Scan_group method) (XRStools.xrs_scans.scangroup method) get_meanegridspacing() (XRStools.xrs_scans.Scan_group method) (XRStools.xrs_scans.scangroup method) get_meanenergy() (XRStools.xrs_scans.Scan_group method) (XRStools.xrs_scans.scangroup method) get_molar_masses() (XRStools.xrs_prediction.sample method) get_murho() (XRStools.xrs_prediction.sample method) get_nff() (XRStools.xrs_utilities.bragg_refl method), [1] get_num_of_MD_steps() (in module XRStools.xrs_utilities), [1]

get_num_of_rois() (XRStools.xrs_scans.Scan method) get_number_of_rois() (XRStools.xrs_rois.roi_object method) get_numofrois() (XRStools.xrs_scans.scan method) get_OO_neighbors() (XRStools.xrs_calctools.xyzBox method) get_OO_neighbors_pbc() (XRStools.xrs_calctools.xyzBox method) get_pixel_range() (XRStools.xrs_utilities.maxipix_det method), [1] get_polarization_factor() (XRStools.xrs_utilities.bragg_refl method), [1] get_polygon_rois() (XRStools.roifinder_and_gui.roi_finder method) get_pw_matrices() (XRStools.xrs_read.Fourc method) (XRStools.xrs_read.Hydra method) get_pzscale() (XRStools.xrs_extraction.valence_CP method) get_q_values() (XRStools.xrs_read.Hydra method) get_raw_data() (XRStools.xrs_read.Fourc method) (XRStools.xrs_read.Hydra method) get_raw_signals() (XRStools.xrs_scans.Scan method) get_reflection_width() (XRStools.xrs_utilities.dtxrd method), [1] get_reflectivity() (XRStools.xrs_prediction.analyzer method) (XRStools.xrs_utilities.bragg_refl method), [1] (XRStools.xrs_utilities.dtxrd method), [1] get_reflectivity_bent() (XRStools.xrs_utilities.bragg_refl method), [1] get_resolution() (XRStools.xrs_scans.Scan method) get_scan_number() (XRStools.xrs_scans.Scan method) get_scannumber() (XRStools.xrs_scans.scan method) get_scans_pw() (in module XRStools.xrs_read) get_shape() (XRStools.xrs_prediction.sample method) (XRStools.xrs_scans.Scan method) (XRStools.xrs_scans.scan method) get_signals() (XRStools.xrs_scans.Scan method) get_size() (XRStools.xrs_prediction.detector method) get_solid_angle() (XRStools.xrs_prediction.analyzer method) get_spectrum() (XRStools.xrs_read.Hydra method) get_spectrum_new() (XRStools.xrs_read.Hydra method) get_stoichiometry() (XRStools.xrs_ComptonProfiles.AtomProfile method) get_stoichWeight() (XRStools.xrs_ComptonProfiles.FormulaProfile method) get_thickness() (XRStools.xrs_prediction.analyzer method) (XRStools.xrs_prediction.detector method) (XRStools.xrs_prediction.sample method) get_thomson_factor() (XRStools.xrs_prediction.thomson method) get_tth() (XRStools.xrs_prediction.compton_profiles method) (XRStools.xrs_prediction.sample method) get_tths() (XRStools.xrs_read.Hydra method) get_type() (XRStools.xrs_scans.Scan method) (XRStools.xrs_scans.scan method) (XRStools.xrs_scans.Scan_group method) (XRStools.xrs_scans.scangroup method) get_UB_Q() (in module XRStools.xrs_utilities), [1] get_x_indices() (XRStools.xrs_rois.roi_object method) get_XES_spectrum() (in module XRStools.xrs_scans) (XRStools.xrs_read.Fourc method) get_y_indices() (XRStools.xrs_rois.roi_object method) get_zoom_rois() (XRStools.roifinder_and_gui.roi_finder method) get_zoom_rois_new() (XRStools.roifinder_and_gui.roi_finder method) getAnglePBCarb() (XRStools.xrs_calctools.xyzAtom method) getAtomicDensity() (in module XRStools.xrs_ComptonProfiles) getAtomicWeight() (in module XRStools.xrs_ComptonProfiles) getCoordinates() (XRStools.xrs_calctools.xyzAtom method) (XRStools.xrs_calctools.xyzBox method) (XRStools.xrs_calctools.xyzMolecule method) getCoordinates_name() (XRStools.xrs_calctools.xyzMolecule method) getDist() (XRStools.xrs_calctools.xyzAtom method) getDistance() (in module XRStools.xrs_calctools) getDistancePbc() (in module XRStools.xrs_calctools) getDistancePBC_arb() (in module XRStools.xrs_calctools) (XRStools.xrs_calctools.xyzBox method) getDistPBCarb() (XRStools.xrs_calctools.xyzAtom method) getDistsFromMolecule() (in module XRStools.xrs_calctools) getDistVector() (in module XRStools.xrs_calctools) getDistVectorPbc() (in module XRStools.xrs_calctools) getDistVectorPBC_arb() (in module XRStools.xrs_calctools) (XRStools.xrs_calctools.xyzBox method) geteloss() (XRStools.xrs_read.read_id20 method) getGeometricCenter() (XRStools.xrs_calctools.xyzMolecule method) getGeometricCenter_arb() (XRStools.xrs_calctools.xyzMolecule method) getNorm() (XRStools.xrs_calctools.xyzAtom method) getpenetrationdepth() (in module XRStools.xrs_utilities), [1] getPeriodicTestBox() (in module XRStools.xrs_calctools) getPeriodicTestBox_arb() (in module XRStools.xrs_calctools) getPeriodicTestBox_molecules() (in module XRStools.xrs_calctools) getqvals() (XRStools.xrs_read.read_id20 method) getqvals_energy() (XRStools.xrs_read.read_id20 method) getrawdata() (XRStools.xrs_read.read_id20 method) getrawdata_pixelwise() (XRStools.xrs_read.read_id20 method) getRDF() (XRStools.xrs_calctools.xyzTrajectory method) getRDF2_arb() (XRStools.xrs_calctools.xyzTrajectory method) getRDF_arb() (XRStools.xrs_calctools.xyzTrajectory method) getspectrum() (XRStools.xrs_read.read_id20 method) getTetraParameter() (in module XRStools.xrs_calctools) (XRStools.xrs_calctools.xyzBox method) getTranslVec() (in module XRStools.xrs_calctools) getTranslVec_geocen() (in module XRStools.xrs_calctools) gettransmission() (in module XRStools.xrs_utilities), [1] gettths() (XRStools.xrs_read.read_id20 method) groBoxParser() (in module XRStools.xrs_calctools) groTrajecParser() (in module XRStools.xrs_calctools)

H

h5_assign_force() (in module XRStools.xrs_rois) help() (in module XRS_swissknife) hex2rgb() (in module XRStools.xrs_utilities), [1] HF_dataset (class in XRStools.xrs_extraction) HFProfile (class in XRStools.xrs_ComptonProfiles)

hlike_Rwfn() (in module XRStools.xrs_utilities), [1] householder() (in module XRStools.xrs_utilities), [1] HRcorrect() (in module XRStools.xrs_ComptonProfiles) (in module XRStools.xrs_utilities), [1] Hydra (class in XRStools.xrs_read) Hydra_imaging (class in XRStools.xrs_read)

I

image (class in XRStools.xrs_imaging) imageset (class in XRStools.xrs_imaging) import_simo_style_rois() (XRStools.roifinder_and_gui.roi_finder method) input_file_parser() (in module XRStools.xrs_prediction) insert_scan() (XRStools.xrs_scans.Scan method) insertScan() (in module XRStools.xrs_scans) interpolate_image() (in module XRStools.xrs_imaging)

interpolate_M() (in module XRStools.xrs_utilities), [1] interpolate_scans() (XRStools.xrs_read.Hydra_imaging method) interpolate_shift_images() (XRStools.xrs_imaging.imageset method) interpolate_xshift_images() (XRStools.xrs_imaging.imageset method) interpolate_yshift_images() (XRStools.xrs_imaging.imageset method) interpolateMatrix() (XRStools.xrs_scans.offDiaDataSet method) is_allowed_refl_fcc() (in module XRStools.xrs_utilities), [1]

K

keithBoxParser() (in module XRStools.xrs_calctools)

L

lindhard_pol() (in module XRStools.xrs_utilities), [1] list_duplicates() (in module XRStools.xrs_ComptonProfiles) load() (XRStools.xrs_imaging.image method) (XRStools.xrs_imaging.imageset method) (XRStools.xrs_imaging.LRimage method) (XRStools.xrs_scans.Scan method) load_erkale_spec() (in module XRStools.xrs_calctools) load_erkale_specs() (in module XRStools.xrs_calctools) load_from_PP() (XRStools.xrs_prediction.radial_wave_function method) load_from_sympy() (XRStools.xrs_prediction.radial_wave_function method) load_hdf5() (XRStools.xrs_scans.offDiaDataSet method) (XRStools.xrs_scans.Scan method) load_loop() (XRStools.xrs_read.Hydra method) load_reference_scan() (XRStools.xrs_read.Hydra_imaging method) load_rois_fromh5() (in module XRStools.xrs_rois) load_rois_fromh5_address() (in module XRStools.xrs_rois) load_rois_fromMasksDict() (XRStools.xrs_rois.roi_object method) load_scan() (XRStools.xrs_read.Fourc method) (XRStools.xrs_read.Hydra method) (XRStools.xrs_read.Hydra_imaging method)

load_shadok_h5() (XRStools.xrs_rois.roi_object method) load_spectrum() (XRStools.xrs_calctools.xyzAtom method) load_spectrum_all_pol() (XRStools.xrs_calctools.xyzAtom method) load_state_hdf5() (XRStools.xrs_imaging.oneD_imaging method) (XRStools.xrs_read.Hydra method) (XRStools.xrs_read.read_id20 method) load_stobe_specs() (in module XRStools.xrs_calctools) loadAXSFtraj() (XRStools.xrs_calctools.xyzTrajectory method) loadelastic() (XRStools.xrs_read.read_id20 method) loadelasticdirect() (XRStools.xrs_read.read_id20 method) loadH5() (XRStools.xrs_rois.roi_object method) loadhe3070() (XRStools.xrs_imaging.imageset method) loadkimberlite() (XRStools.xrs_imaging.imageset method) loadlong() (XRStools.xrs_read.read_id20 method) loadlongdirect() (XRStools.xrs_read.read_id20 method) loadloop() (XRStools.xrs_read.read_id20 method) loadloopdirect() (XRStools.xrs_read.read_id20 method) loadscan() (XRStools.xrs_read.read_id20 method) loadscan_2Dimages() (XRStools.xrs_imaging.oneD_imaging method) loadscandirect() (XRStools.xrs_read.read_id20 method) LRimage (class in XRStools.xrs_imaging)

M

main() (in module XRStools.xrs_prediction) make_scan_group_pixel() (in module XRStools.xrs_scans) make_scan_group_sum() (in module XRStools.xrs_scans) makegroup() (in module XRStools.xrs_scans) makegroup_nointerp() (in module XRStools.xrs_scans) makeprofile() (in module XRStools.xrs_utilities), [1] makeprofile_comp() (in module XRStools.xrs_utilities), [1] makeprofile_compds() (in module XRStools.xrs_utilities), [1] makepzprofile() (in module XRStools.xrs_utilities), [1] map_chamber_names() (in module XRStools.xrs_extraction) mapShellNames() (in module XRStools.xrs_ComptonProfiles) mat2con() (in module XRStools.xrs_utilities), [1] mat2vec() (in module XRStools.xrs_utilities), [1] matrix_element (class in XRStools.xrs_prediction) maxipix_det (class in XRStools.xrs_utilities), [1] merge_roi_objects_by_matrix() (in module XRStools.xrs_rois) module XRS_swissknife, [1], [2], [3], [4] XRStools.__init__ XRStools.roifinder_and_gui XRStools.xrs_calctools XRStools.xrs_ComptonProfiles XRStools.xrs_extraction XRStools.xrs_fileIO XRStools.xrs_imaging XRStools.xrs_prediction XRStools.xrs_read XRStools.xrs_rois XRStools.xrs_scans XRStools.xrs_utilities, [1]

momtrans_au() (in module XRStools.xrs_utilities), [1] momtrans_inva() (in module XRStools.xrs_utilities), [1] mpr() (in module XRStools.xrs_utilities), [1] mpr_compds() (in module XRStools.xrs_utilities), [1] multiplyBoxPBC() (XRStools.xrs_calctools.xyzBox method) multiplyBoxPBC_arb() (XRStools.xrs_calctools.xyzBox method) myEdfRead() (in module XRStools.xrs_fileIO) myprho() (in module XRStools.xrs_utilities), [1]

N

NNMFcost() (in module XRStools.xrs_utilities), [1] NNMFcost_der() (in module XRStools.xrs_utilities), [1] NNMFcost_old() (in module XRStools.xrs_utilities), [1] nonzeroavg() (in module XRStools.xrs_utilities), [1] norm_area() (XRStools.xrs_calctools.erkale method) (XRStools.xrs_calctools.stobe method)

norm_max() (XRStools.xrs_calctools.erkale method) normalizationDict (XRStools.xrs_scans.Scan attribute) normalize_arb_spectrum() (XRStools.xrs_calctools.xyzBox method) normalize_spectrum() (XRStools.xrs_calctools.xyzAtom method) (XRStools.xrs_calctools.xyzBox method) normalizeRC() (XRStools.xrs_scans.offDiaDataSet method) normalizeSignals() (XRStools.xrs_scans.offDiaDataSet method)

O

odefctn() (in module XRStools.xrs_utilities), [1] odefctn_CN() (in module XRStools.xrs_utilities), [1] offDiaDataSet (class in XRStools.xrs_scans) OG_dec() (in module XRStools.xrs_rois) OG_inc() (in module XRStools.xrs_rois)

Omega() (in module XRStools.xrs_utilities), [1] oneD_imaging (class in XRStools.xrs_imaging) order_generator_ascending() (in module XRStools.xrs_rois) order_generator_descending() (in module XRStools.xrs_rois) orderrois() (XRStools.xrs_read.read_id20 method)

P

parseChemFormula() (in module XRStools.xrs_ComptonProfiles) parseformula() (in module XRStools.xrs_utilities), [1] parseOCEANinputFile() (in module XRStools.xrs_calctools) parsePwscfFile() (in module XRStools.xrs_calctools) parseVaspFile() (in module XRStools.xrs_calctools) parseXYZfile() (in module XRStools.xrs_calctools) Phi() (in module XRStools.xrs_utilities), [1] plot_abs_cross_section() (XRStools.xrs_prediction.absolute_cross_section method) plot_HF_profile() (XRStools.xrs_prediction.compton_profiles method) plot_inv_absorption() (XRStools.xrs_prediction.sample method) plot_reflectivity() (XRStools.xrs_prediction.analyzer method) plot_spec() (XRStools.xrs_calctools.erkale method) plotimage() (XRStools.xrs_imaging.image method) (XRStools.xrs_imaging.LRimage method) plotLR() (XRStools.xrs_imaging.imageset method)

plotpenetrationdepth() (in module XRStools.xrs_utilities), [1] plotSR() (XRStools.xrs_imaging.imageset method) plottransmission() (in module XRStools.xrs_utilities), [1] pop() (XRStools.xrs_rois.roi_object method) popAtom() (XRStools.xrs_calctools.xyzMolecule method) PrepareEdfMatrix() (in module XRStools.xrs_fileIO) PrepareEdfMatrix_TwoImages() (in module XRStools.xrs_fileIO) primtoconv() (in module XRStools.xrs_utilities), [1] print_citation_message() (in module XRStools.xrs_read) print_scan_length() (XRStools.xrs_read.Hydra method) printlength() (XRStools.xrs_read.read_id20 method) PyMcaEdfRead() (in module XRStools.xrs_fileIO) PyMcaSpecRead() (in module XRStools.xrs_fileIO) PyMcaSpecRead_my() (in module XRStools.xrs_fileIO) pz2e1() (in module XRStools.xrs_utilities), [1] PzProfile() (in module XRStools.xrs_ComptonProfiles)

R

radial_wave_function (class in XRStools.xrs_prediction) RC_interp_functor (class in XRStools.xrs_scans) read_dft_wfn() (in module XRStools.xrs_utilities), [1] read_id20 (class in XRStools.xrs_read) read_just_first_scanimage() (XRStools.xrs_read.read_id20 method) readbiggsdata() (in module XRStools.xrs_fileIO) (in module XRStools.xrs_utilities), [1] ReadEdf_justFirstImage() (in module XRStools.xrs_fileIO) ReadEdfImages() (in module XRStools.xrs_fileIO) ReadEdfImages_my() (in module XRStools.xrs_fileIO) ReadEdfImages_PyMca() (in module XRStools.xrs_fileIO) ReadEdfImages_TwoImages() (in module XRStools.xrs_fileIO) readfio() (in module XRStools.xrs_utilities), [1] readp01image() (in module XRStools.xrs_utilities), [1] readp01scan() (in module XRStools.xrs_utilities), [1] readp01scan_rep() (in module XRStools.xrs_utilities), [1] readscan() (XRStools.xrs_read.read_id20 method) readscan_new() (XRStools.xrs_read.read_id20 method) ReadScanFromFile() (in module XRStools.xrs_fileIO) readxas() (in module XRStools.xrs_calctools) refine_pw_rois() (XRStools.roifinder_and_gui.roi_finder method) refine_rois_CW() (XRStools.roifinder_and_gui.roi_finder method) refine_rois_CW_old() (XRStools.roifinder_and_gui.roi_finder method) refine_rois_MF() (XRStools.roifinder_and_gui.roi_finder method)

refine_rois_MF_new() (XRStools.roifinder_and_gui.roi_finder method) refine_rois_PW() (XRStools.roifinder_and_gui.roi_finder method) refine_rois_PW_old() (XRStools.roifinder_and_gui.roi_finder method) refine_rois_RW() (XRStools.roifinder_and_gui.roi_finder method) refine_rois_RW_old() (XRStools.roifinder_and_gui.roi_finder method) removeBackgroundRoi() (XRStools.xrs_read.read_id20 method) removeConstBack() (XRStools.xrs_scans.offDiaDataSet method) removeCorePearsonAv() (XRStools.xrs_extraction.edge_extraction method) removeCorePearsonAv_new() (XRStools.xrs_extraction.edge_extraction method) removeElastic() (XRStools.xrs_scans.offDiaDataSet method) removeElastic2() (XRStools.xrs_scans.offDiaDataSet method) removeLinearBack() (XRStools.xrs_scans.offDiaDataSet method) removePearsonAv() (XRStools.xrs_extraction.edge_extraction method) removePearsonBack() (XRStools.xrs_scans.offDiaDataSet method) removePolyCoreAv() (XRStools.xrs_extraction.edge_extraction method) repair_h2o_molecules_pbc() (in module XRStools.xrs_calctools) replaceSignalByConstant() (XRStools.xrs_scans.offDiaDataSet method) roi_finder (class in XRStools.roifinder_and_gui) roi_object (class in XRStools.xrs_rois) roi_widget() (XRStools.roifinder_and_gui.roi_finder method) run() (in module XRStools.xrs_prediction) Rx() (in module XRStools.xrs_utilities), [1] Ry() (in module XRStools.xrs_utilities), [1] Rz() (in module XRStools.xrs_utilities), [1]

S

sample (class in XRStools.xrs_prediction) save() (XRStools.xrs_imaging.image method) (XRStools.xrs_imaging.imageset method) (XRStools.xrs_imaging.LRimage method) save_average_Sqw() (XRStools.xrs_extraction.edge_extraction method) save_hdf5() (XRStools.xrs_prediction.absolute_cross_section method) (XRStools.xrs_scans.offDiaDataSet method) (XRStools.xrs_scans.Scan method) save_raw_data() (XRStools.xrs_read.read_id20 method) save_state() (XRStools.xrs_read.read_id20 method) save_state_hdf5() (XRStools.xrs_imaging.oneD_imaging method) (XRStools.xrs_read.Hydra method) (XRStools.xrs_read.read_id20 method) save_txt() (XRStools.xrs_prediction.absolute_cross_section method) savitzky_golay() (in module XRStools.xrs_utilities), [1] Scan (class in XRStools.xrs_scans) scan (class in XRStools.xrs_scans) Scan_group (class in XRStools.xrs_scans) scangroup (class in XRStools.xrs_scans) scatterPlot() (XRStools.xrs_calctools.xyzBox method) (XRStools.xrs_calctools.xyzMolecule method) set_asymmetry() (XRStools.xrs_utilities.dtxrd method), [1] set_bend_r() (XRStools.xrs_prediction.analyzer method) set_diced() (XRStools.xrs_prediction.analyzer method) set_energy() (XRStools.xrs_prediction.detector method) (XRStools.xrs_utilities.dtxrd method), [1] set_hkl() (XRStools.xrs_prediction.analyzer method) (XRStools.xrs_utilities.dtxrd method), [1] set_mask_d() (XRStools.xrs_prediction.analyzer method) set_material() (XRStools.xrs_prediction.analyzer method) (XRStools.xrs_prediction.detector method) set_roiObj() (XRStools.xrs_read.Fourc method) (XRStools.xrs_read.Hydra method) (XRStools.xrs_read.read_id20 method) set_size() (XRStools.xrs_prediction.detector method) set_thickness() (XRStools.xrs_prediction.analyzer method) (XRStools.xrs_prediction.detector method)

setBoxLength() (XRStools.xrs_calctools.xyzBox method) sgolay2d() (in module XRStools.xrs_utilities), [1] shift() (XRStools.xrs_rois.roi_object method) shift_roi_indices() (in module XRStools.xrs_rois) shiftx() (XRStools.xrs_imaging.image method) (XRStools.xrs_imaging.LRimage method) shifty() (XRStools.xrs_imaging.image method) (XRStools.xrs_imaging.LRimage method) show() (XRStools.xrs_rois.roi_object method) show_rois() (in module XRStools.roifinder_and_gui) (XRStools.roifinder_and_gui.roi_finder method) sigmainc() (in module XRStools.xrs_utilities), [1] SilxSpecRead() (in module XRStools.xrs_fileIO) sorter() (in module XRStools.xrs_calctools) SpecRead() (in module XRStools.xrs_fileIO) specread() (in module XRStools.xrs_utilities), [1] spline2() (in module XRStools.xrs_calctools) (in module XRStools.xrs_utilities), [1] split_hdf5_address() (in module XRStools.xrs_utilities), [1] SqwPredict (class in XRStools.xrs_ComptonProfiles) stiff_compl_matrix_Si() (in module XRStools.xrs_utilities), [1] stitch_groups_to_spectrum() (in module XRStools.xrs_scans) stobe (class in XRStools.xrs_calctools) strip() (XRStools.xrs_rois.roi_object method) sum_scans_to_group() (in module XRStools.xrs_scans) sum_specs() (XRStools.xrs_calctools.erkale method) (XRStools.xrs_calctools.stobe method) SumDirect() (XRStools.xrs_read.Fourc method) (XRStools.xrs_read.Hydra method) (XRStools.xrs_read.read_id20 method) sumx() (in module XRStools.xrs_utilities), [1] superR_fit_responses() (in module XRS_swissknife) superR_recreate_rois() (in module XRS_swissknife) superR_scal_deltaXimages() (in module XRS_swissknife) svd_my() (in module XRStools.xrs_utilities), [1] swap_indices_old_rois() (in module XRStools.xrs_rois)

T

taupgen() (in module XRStools.xrs_utilities), [1] taupgen_amplitude() (in module XRStools.xrs_utilities), [1] tauphoto() (in module XRStools.xrs_utilities), [1] test_roifinder() (in module XRStools.roifinder_and_gui) there_is_a_valid_roi_at() (XRStools.xrs_read.Hydra method) (XRStools.xrs_read.read_id20 method) thomson (class in XRStools.xrs_prediction)

translateAtomsMinimumImage() (XRStools.xrs_calctools.xyzBox method) (XRStools.xrs_calctools.xyzMolecule method) translateOcean2FDMNES_p1() (in module XRStools.xrs_calctools) translateSelf() (XRStools.xrs_calctools.xyzAtom method) (XRStools.xrs_calctools.xyzMolecule method) translateSelf_arb() (XRStools.xrs_calctools.xyzAtom method) trapz_weights() (in module XRStools.xrs_ComptonProfiles) TTsolver1D() (in module XRStools.xrs_utilities), [1]

U

unconstrained_mf() (in module XRStools.xrs_utilities), [1]

V

valence_CP (class in XRStools.xrs_extraction) vangle() (in module XRStools.xrs_utilities), [1] vaspBoxParser() (in module XRStools.xrs_calctools)

vaspTrajecParser() (in module XRStools.xrs_calctools) vec2mat() (in module XRStools.xrs_utilities), [1] vrot() (in module XRStools.xrs_utilities), [1] vrot2() (in module XRStools.xrs_utilities), [1]

W

windowSignalMatrix() (XRStools.xrs_scans.offDiaDataSet method) write_ascii() (XRStools.xrs_prediction.matrix_element method) write_H5() (XRStools.xrs_prediction.matrix_element method) write_rois_toh5() (in module XRStools.xrs_rois) write_rois_toh5_for_resynth() (in module XRStools.xrs_rois) writeBox() (XRStools.xrs_calctools.xyzBox method) writeClusters() (XRStools.xrs_calctools.xyzBox method) writeClusters_arb() (XRStools.xrs_calctools.xyzBox method) writeFDMNESinput() (XRStools.xrs_calctools.xyzBox method) writeFDMNESinput_file() (in module XRStools.xrs_calctools) writeFEFFinput_arb() (in module XRStools.xrs_calctools) writeH2Oclusters() (XRStools.xrs_calctools.xyzBox method) writeH5() (XRStools.xrs_rois.roi_object method) writeMD1Input() (in module XRStools.xrs_calctools) writeMoleculeCluster() (XRStools.xrs_calctools.xyzBox method)

writeOCEAN_XESInput() (in module XRStools.xrs_calctools) writeOCEANinput() (in module XRStools.xrs_calctools) (XRStools.xrs_calctools.xyzBox method) writeOCEANinput_arb() (in module XRStools.xrs_calctools) writeOCEANinput_full() (in module XRStools.xrs_calctools) writeOCEANinput_new() (in module XRStools.xrs_calctools) writePWinuptFile() (in module XRStools.xrs_calctools) writeRandBox() (XRStools.xrs_calctools.xyzTrajectory method) writeRelBox() (XRStools.xrs_calctools.xyzBox method) writeRelXYZfile() (in module XRStools.xrs_calctools) WriteScanToFile() (in module XRStools.xrs_fileIO) writeWFN1waterInput() (in module XRStools.xrs_calctools) writeXYZfile() (in module XRStools.xrs_calctools) (XRStools.xrs_calctools.xyzMolecule method) writeXYZtraj() (XRStools.xrs_calctools.xyzTrajectory method) writeXYZtrajectory() (in module XRStools.xrs_calctools)

X

xas_fluo_correct() (in module XRStools.xrs_utilities), [1] XRS_swissknife module, [1], [2], [3], [4] XRStools.__init__ module XRStools.roifinder_and_gui module XRStools.xrs_calctools module XRStools.xrs_ComptonProfiles module XRStools.xrs_extraction module XRStools.xrs_fileIO module XRStools.xrs_imaging module

XRStools.xrs_prediction module XRStools.xrs_read module XRStools.xrs_rois module XRStools.xrs_scans module XRStools.xrs_utilities module, [1] xyzAtom (class in XRStools.xrs_calctools) xyzBox (class in XRStools.xrs_calctools) xyzMolecule (class in XRStools.xrs_calctools) xyzTrajecParser() (in module XRStools.xrs_calctools) xyzTrajectory (class in XRStools.xrs_calctools)