Index

A

addLabelsOnPlot() (in module cima.utils.visualization) align_2seqs() (in module cima.utils.vector) all_labels (cima.detection.clusters.HDBSCAN_stable attribute) alpha_shape_3D() (cima.segments.segment_convex.TransformConvex method) altTorsion() (in module cima.utils.vector) areCoordsInMapBox() (cima.segments.segment_gaussian.TransformBlurrer static method)

arg() (cima.utils.vector.Vector method) ari_median (cima.detection.clusters.HDBSCAN_stable attribute) ari_var (cima.detection.clusters.HDBSCAN_stable attribute) Assessment_Chrom_Precision() (in module cima.assessment.images_assessment) axis_angle_to_euler() (in module cima.utils.vector) axis_angle_to_matrix() (in module cima.utils.vector)

B

BeadsFinder (class in cima.detection.beads_identification) best_ind (cima.detection.clusters.HDBSCAN_stable attribute)

best_mcs (cima.detection.clusters.HDBSCAN_stable attribute) box_size() (cima.maps.emmap.Map method)

C

calcMtrx() (in module cima.utils.vector) calculate_centre_of_mass() (cima.segments.segment_info_xyz.SegmentXYZ method) calculate_centroid() (cima.segments.segment_info_xyz.SegmentXYZ method) calculate_map_threshold_SR() (in module cima.maps.density_properties) calculate_rmsd_matrix() (in module cima.utils.misc) CCC_map() (cima.maps.scoring_functions.ScoringFunctions method) centre() (cima.maps.emmap.Map method) change_origin() (cima.maps.emmap.Map method) ChromosomesIDs() (cima.segments.segment_info.Segment method) cima module cima.assessment module cima.assessment.images_assessment module cima.detection module cima.detection.beads_identification module cima.detection.clusters module cima.maps module cima.maps.density_properties module cima.maps.emmap module cima.maps.map_features module cima.maps.map_parser module cima.maps.map_spatial_features module cima.maps.maptomap module cima.maps.scoring_functions module cima.maps.structure_blurrer module cima.maps.vq module cima.parsers module cima.parsers.parser_csv module cima.parsers.parser_h5py module cima.patches module cima.patches.homolog_separator module cima.patches.nuclear_mask module cima.patches.segment_reconstruction module

cima.segments module cima.segments.segment_convex module cima.segments.segment_features module cima.segments.segment_gaussian module cima.segments.segment_info module cima.segments.segment_info_h5 module cima.segments.segment_info_xyz module cima.segments.segment_spatial_features module cima.utils module cima.utils.matrices_comparison module cima.utils.misc module cima.utils.stats_function module cima.utils.vector module cima.utils.visualization module cima.utils.walk_features module cima.utils.write_pdb module compute_rmsd() (in module cima.utils.matrices_comparison) (in module cima.utils.misc) convertToFreq() (in module cima.utils.walk_features) convertToMatrix() (in module cima.utils.walk_features) convertToMatrix2() (in module cima.utils.walk_features) copy() (cima.detection.clusters.DBscan_grid_search_stable method) (cima.detection.clusters.HDBSCAN_stable method) (cima.maps.emmap.Map method) (cima.segments.segment_info.Segment method) (cima.segments.segment_info_h5.SegmentH5 method) (cima.segments.segment_info_xyz.SegmentXYZ method) (cima.utils.vector.Vector method) copyWithNewContent() (cima.segments.segment_info.Segment method) (cima.segments.segment_info_h5.SegmentH5 method) (cima.segments.segment_info_xyz.SegmentXYZ method) cps() (in module cima.utils.vector) Create_Random_Hom_Ratio() (in module cima.utils.stats_function) Create_Random_Hom_Ratio_largeroversmaller() (in module cima.utils.stats_function) Create_Random_Hom_Ratio_Paternal_Origin() (in module cima.utils.stats_function) Create_Random_Hom_Ratio_smalloverlarger() (in module cima.utils.stats_function) CropBox() (in module cima.maps.density_properties) cross() (cima.utils.vector.Vector method) CSVParser (class in cima.parsers.parser_csv) Cycle_assessment() (in module cima.assessment.images_assessment)

D

DBscan() (in module cima.detection.clusters) DBscan_grid_search_stable (class in cima.detection.clusters) Decoder (class in cima.patches.segment_reconstruction)

dist() (cima.utils.vector.Vector method) DistanceBetweenSegments() (in module cima.maps.map_spatial_features) dot() (cima.utils.vector.Vector method) downsample_map() (cima.maps.emmap.Map method)

E

EntanglementBetweenSegments() (in module cima.maps.map_spatial_features) envelope_score() (cima.maps.scoring_functions.ScoringFunctions method)

envelope_score_map() (cima.maps.scoring_functions.ScoringFunctions method) euler_to_matrix() (in module cima.utils.vector)

F

feats_df (cima.detection.clusters.ThresholdClusterFilter attribute) features_to_use (cima.detection.clusters.ThresholdClusterFilter attribute) find_column_names() (in module cima.utils.misc) fit() (cima.detection.beads_identification.BeadsFinder method) (cima.detection.clusters.DBscan_grid_search_stable method) (cima.detection.clusters.HDBSCAN_stable method) (cima.detection.clusters.ThresholdClusterFilter method) (cima.patches.homolog_separator.HomologSeparator method) (cima.patches.segment_reconstruction.Decoder method)

fof_bs_ct_reader() (in module cima.utils.misc) fof_volumetric_ct_reader() (in module cima.utils.misc) fof_volumetric_ct_writer() (in module cima.utils.misc) fourier_transform() (cima.maps.emmap.Map method) FSC_betweenMaps() (cima.maps.scoring_functions.ScoringFunctions method) func() (in module cima.utils.stats_function) func2() (in module cima.utils.stats_function) func_inverse1() (in module cima.utils.stats_function) func_powerlaw() (in module cima.utils.stats_function) func_sqrt() (in module cima.utils.stats_function)

G

gaussian_blur() (cima.maps.structure_blurrer.StructureBlurrer method) gaussian_blur_box() (cima.maps.structure_blurrer.StructureBlurrer method) gaussian_blur_real_space() (cima.maps.structure_blurrer.StructureBlurrer method) gaussian_blur_real_space_box() (cima.maps.structure_blurrer.StructureBlurrer method) get_binarized_points() (in module cima.maps.density_properties) get_Chromosomes_segment() (cima.segments.segment_info.Segment method) get_Cluster_segment() (cima.segments.segment_info_xyz.SegmentXYZ method) get_com() (cima.maps.emmap.Map method) get_contour_points() (in module cima.maps.density_properties) get_coordinates() (cima.maps.structure_blurrer.StructureBlurrer method) get_dtype_dict() (in module cima.utils.misc) get_endian() (cima.maps.map_parser.MapParser static method) get_extreme_values() (cima.segments.segment_info_xyz.SegmentXYZ method) get_index_points() (in module cima.maps.density_properties) get_indices() (cima.maps.structure_blurrer.StructureBlurrer method) get_line_between_points() (cima.maps.emmap.Map method) get_multiple_Time_segment() (cima.segments.segment_info_xyz.SegmentXYZ method) get_normal_vector() (cima.maps.emmap.Map method) get_partial_DLSF() (cima.maps.scoring_functions.ScoringFunctions method) get_point_map() (cima.maps.emmap.Map method) get_pos() (cima.maps.emmap.Map method) get_primary_boundary() (cima.maps.emmap.Map method) get_rgyration() (in module cima.segments.segment_features) get_second_boundary() (cima.maps.emmap.Map method) get_significant_points() (cima.maps.emmap.Map method) get_Time_segment() (cima.segments.segment_info_xyz.SegmentXYZ method) get_vector_list() (cima.segments.segment_info_xyz.SegmentXYZ method) get_vectors() (cima.maps.emmap.Map method) get_VQ_points() (in module cima.maps.vq) GetArea_abovecontour() (in module cima.maps.map_features) GetArea_equivalent_diameter() (in module cima.maps.map_features) getBinaryMap() (cima.maps.emmap.Map method) getClassicalCompactness() (in module cima.maps.map_features) getClusters() (cima.segments.segment_info_xyz.SegmentXYZ method) getCoM() (in module cima.utils.visualization) getCOMDistance() (in module cima.segments.segment_spatial_features) getConvexHullVolume() (in module cima.maps.map_features) getConvexity() (in module cima.maps.map_features) getConvexMap() (in module cima.maps.map_features) Getcoord() (cima.segments.segment_info_xyz.SegmentXYZ method) getCoordsRelativeToMap() (cima.segments.segment_gaussian.TransformBlurrer static method) getCoordsRelativeToMapWithOriginalAxesOrder() (cima.segments.segment_gaussian.TransformBlurrer static method) getCustomColormap() (in module cima.utils.visualization) getDiagValidCounts() (cima.utils.matrices_comparison.SCCComputer method) getDiscreteCompactness() (in module cima.maps.map_features)

GetEccenticity_abovecontour() (in module cima.maps.map_features) GetEccentricity() (in module cima.segments.segment_features) getEfficacy() (cima.patches.segment_reconstruction.Decoder method) getEigenvecsFromContactMat() (in module cima.utils.walk_features) GetEllipticity() (in module cima.segments.segment_features) GetEllipticity_abovecontour() (in module cima.maps.map_features) getFilledMap() (cima.maps.emmap.Map method) getFrames() (cima.segments.segment_info.Segment method) getHolelessSolidity() (in module cima.maps.map_features) getInRange() (cima.segments.segment_info_xyz.SegmentXYZ method) GetLocalisationOverlap() (in module cima.segments.segment_spatial_features) getLogLinearRegression() (in module cima.utils.matrices_comparison) (in module cima.utils.stats_function) getMap() (cima.maps.emmap.Map method) getMapRelativePointsFromMap() (in module cima.maps.map_features) getMapsOverlap() (cima.maps.scoring_functions.ScoringFunctions static method) getMapWithAttributeOverlayed() (cima.segments.segment_gaussian.TransformBlurrer static method) GetMaxAccuracy() (cima.segments.segment_info.Segment method) GetMaxPrecision() (cima.segments.segment_info.Segment method) GetMeanAccuracy() (cima.segments.segment_info.Segment method) getMeanDistance() (in module cima.segments.segment_spatial_features) GetMeanPrecision() (cima.segments.segment_info.Segment method) getMergedMorphologicalAndSpatialSegmentsFeatures() (in module cima.utils.walk_features) GetMinAccuracy() (cima.segments.segment_info.Segment method) getMinDistance() (in module cima.segments.segment_spatial_features) GetMinPrecision() (cima.segments.segment_info.Segment method) getMVEE() (in module cima.segments.segment_features) getMVEEEccentricity() (in module cima.segments.segment_features) getMVEEEllipticity() (in module cima.segments.segment_features) getPointsFromMap() (in module cima.maps.map_features) getPointwiseDensity() (in module cima.detection.clusters) getPortion() (cima.segments.segment_info_xyz.SegmentXYZ method) getSegmentFeatures() (in module cima.utils.walk_features) getSegmentMetadata() (in module cima.utils.walk_features) getSegmentsFeatures() (in module cima.utils.walk_features) getSegmentsMetadata() (in module cima.utils.walk_features) getSegmentsPairFeatures() (in module cima.utils.walk_features) getSolidity() (in module cima.maps.map_features) GetSparseness() (in module cima.maps.map_features) getSpatialFeaturesInterWalk() (in module cima.utils.walk_features) getSpatialFeaturesIntraWalk() (in module cima.utils.walk_features) GetSphericity() (in module cima.maps.map_features) GetSphericity_bribiesca() (in module cima.maps.map_features) getSurfaceDistance() (in module cima.maps.map_spatial_features) GetVolume_abovecontour() (in module cima.maps.map_features) GetVolume_equivalent_diameter() (in module cima.maps.map_features)

H

h5pyParser (class in cima.parsers.parser_h5py) hard_sphere() (cima.maps.structure_blurrer.StructureBlurrer method) hard_sphere_box() (cima.maps.structure_blurrer.StructureBlurrer method)

HDBSCAN_stable (class in cima.detection.clusters) header_to_binary() (cima.maps.emmap.Map method) Hist_density() (in module cima.maps.density_properties) HomologSeparator (class in cima.patches.homolog_separator)

L

labels_ (cima.detection.clusters.HDBSCAN_stable attribute) (cima.patches.homolog_separator.HomologSeparator attribute) laplace_CCC() (cima.maps.scoring_functions.ScoringFunctions method)

laplace_filtered() (cima.maps.emmap.Map method) limits (cima.detection.clusters.ThresholdClusterFilter attribute) load() (cima.patches.segment_reconstruction.Decoder method) LSF() (cima.maps.scoring_functions.ScoringFunctions method)

M

make_atom_overlay_map() (cima.maps.structure_blurrer.StructureBlurrer method) make_atom_overlay_map1() (cima.maps.structure_blurrer.StructureBlurrer method) make_atom_overlay_mapB() (cima.maps.structure_blurrer.StructureBlurrer method) make_bin_map() (cima.maps.emmap.Map method) makeAxesLabelsLog() (in module cima.utils.matrices_comparison) (in module cima.utils.stats_function) makeKDTree() (cima.maps.emmap.Map method) Map (class in cima.maps.emmap) Map2Map() (in module cima.maps.maptomap) map_points() (in module cima.maps.vq) map_rotate_by_axis_angle() (cima.maps.emmap.Map method) map_size() (cima.maps.emmap.Map method) mapGridPosition() (cima.maps.structure_blurrer.StructureBlurrer method) mapGridPositions() (cima.maps.structure_blurrer.StructureBlurrer method) mapGridPositions_vdw() (cima.maps.structure_blurrer.StructureBlurrer method) MapParser (class in cima.maps.map_parser) maptree() (cima.maps.structure_blurrer.StructureBlurrer method) MaskCountour() (in module cima.maps.density_properties) matrix_transform() (cima.maps.emmap.Map method) (cima.utils.vector.Vector method) max() (cima.maps.emmap.Map method) mean() (cima.maps.emmap.Map method) MeanMatrix() (in module cima.utils.walk_features) median() (cima.maps.emmap.Map method) mergeOtherDBSCANGrid() (cima.detection.clusters.DBscan_grid_search_stable method) mergeOtherHDBSCANGrid() (cima.detection.clusters.HDBSCAN_stable method) MI() (cima.maps.scoring_functions.ScoringFunctions method) min() (cima.maps.emmap.Map method) min_cluster_size_range (cima.detection.clusters.HDBSCAN_stable attribute) mod() (cima.utils.vector.Vector method) model_tree() (cima.maps.structure_blurrer.StructureBlurrer method) module cima cima.assessment cima.assessment.images_assessment cima.detection cima.detection.beads_identification cima.detection.clusters cima.maps cima.maps.density_properties cima.maps.emmap cima.maps.map_features cima.maps.map_parser cima.maps.map_spatial_features cima.maps.maptomap cima.maps.scoring_functions cima.maps.structure_blurrer cima.maps.vq cima.parsers cima.parsers.parser_csv cima.parsers.parser_h5py cima.patches cima.patches.homolog_separator cima.patches.nuclear_mask cima.patches.segment_reconstruction cima.segments cima.segments.segment_convex cima.segments.segment_features cima.segments.segment_gaussian cima.segments.segment_info cima.segments.segment_info_h5 cima.segments.segment_info_xyz cima.segments.segment_spatial_features cima.utils cima.utils.matrices_comparison cima.utils.misc cima.utils.stats_function cima.utils.vector cima.utils.visualization cima.utils.walk_features cima.utils.write_pdb

N

new_labels (cima.detection.clusters.ThresholdClusterFilter attribute) no_of_Chromosomes() (cima.segments.segment_info.Segment method) no_of_Cluster() (cima.segments.segment_info_xyz.SegmentXYZ method)

no_of_Times() (cima.segments.segment_info_xyz.SegmentXYZ method) normal_vector_score() (cima.maps.scoring_functions.ScoringFunctions method) normalise() (cima.maps.emmap.Map method)

O

optimal_segment (cima.detection.clusters.HDBSCAN_stable attribute) OrderbyExperimenttime() (cima.segments.segment_info.Segment method)

ordered_params_df (cima.detection.clusters.HDBSCAN_stable attribute) origin_change_maps() (cima.maps.emmap.Map method)

P

pad_map() (cima.maps.emmap.Map method) pearson_corr() (in module cima.utils.matrices_comparison) PhotonCount_Filter() (cima.segments.segment_info.Segment method) pixel_centre() (cima.maps.emmap.Map method) plot() (cima.detection.clusters.ThresholdClusterFilter method) plot3DConvexHull() (in module cima.utils.visualization) plot3DMapAsCubes() (in module cima.utils.visualization) plot3DMapAsPoints() (in module cima.utils.visualization) plot3DMapMarchingCubes() (in module cima.utils.visualization) plot3DMultipleMapsMarchingCubes() (in module cima.utils.visualization) plotAriGrid() (cima.detection.clusters.DBscan_grid_search_stable method) (cima.detection.clusters.HDBSCAN_stable method) plotAriVarGrid() (cima.detection.clusters.DBscan_grid_search_stable method) (cima.detection.clusters.HDBSCAN_stable method) plotClustering2DProjections() (in module cima.utils.visualization)

plotClustering3D() (in module cima.utils.visualization) plotDecodingTrace() (in module cima.utils.visualization) plotDecodingWithSpecifiedColors() (in module cima.utils.visualization) plotEfficacyTable() (cima.patches.segment_reconstruction.Decoder method) plotEfficacyTableWithUncertainty() (cima.patches.segment_reconstruction.Decoder method) plotEfficacyTableWithVolume() (cima.patches.segment_reconstruction.Decoder method) plotLine() (in module cima.utils.matrices_comparison) (in module cima.utils.stats_function) plotLogWithKdeColors() (in module cima.utils.matrices_comparison) (in module cima.utils.stats_function) power_law() (in module cima.utils.stats_function) PrecisionFilter() (cima.segments.segment_info.Segment method) protMap() (cima.maps.structure_blurrer.StructureBlurrer method) protMapBox() (cima.maps.structure_blurrer.StructureBlurrer method) PSFz_shiftFilter() (cima.segments.segment_info.Segment method)

R

random_vector() (in module cima.utils.vector) random_vector2() (in module cima.utils.vector) read_CSV_file() (cima.parsers.parser_csv.CSVParser static method) read_step_from_CSV_file() (cima.parsers.parser_csv.CSVParser static method) readH5File() (cima.parsers.parser_h5py.h5pyParser static method) readMRC() (cima.maps.map_parser.MapParser static method) readMRCHeader() (cima.maps.map_parser.MapParser static method) removeNoise() (cima.segments.segment_info_xyz.SegmentXYZ method) renumber_Time() (cima.segments.segment_info_xyz.SegmentXYZ method) renumberTimeFromInt() (cima.segments.segment_info_xyz.SegmentXYZ method)

representSingleLocalization() (cima.segments.segment_info.Segment static method) (cima.segments.segment_info_h5.SegmentH5 static method) (cima.segments.segment_info_xyz.SegmentXYZ static method) resample_by_apix() (cima.maps.emmap.Map method) resample_by_box_size() (cima.maps.emmap.Map method) resize_map() (cima.maps.emmap.Map method) retained_clusters_ids (cima.detection.clusters.ThresholdClusterFilter attribute) reverse() (cima.utils.vector.Vector method) rotate_by_axis_angle() (cima.maps.emmap.Map method) rotate_by_euler() (cima.maps.emmap.Map method) rotate_by_matrix() (cima.maps.emmap.Map method)

S

Saturation_by_experiment_pseudotime() (in module cima.assessment.images_assessment) Saturation_to_final_structure() (in module cima.assessment.images_assessment) saveLog() (cima.detection.clusters.DBscan_grid_search_stable method) (cima.detection.clusters.HDBSCAN_stable method) scale_map() (cima.maps.emmap.Map method) scc() (in module cima.utils.matrices_comparison) sccByDiag2() (cima.utils.matrices_comparison.SCCComputer method) sccByDiagOriginal() (cima.utils.matrices_comparison.SCCComputer method) SCCComputer (class in cima.utils.matrices_comparison) ScoringFunctions (class in cima.maps.scoring_functions) search_epsilon() (in module cima.detection.clusters) segment (cima.detection.clusters.HDBSCAN_stable attribute) Segment (class in cima.segments.segment_info) SegmentH5 (class in cima.segments.segment_info_h5) SegmentXYZ (class in cima.segments.segment_info_xyz) set_chromosomes() (cima.segments.segment_info.Segment method)

set_cluster_ids() (cima.segments.segment_info_xyz.SegmentXYZ method) shift_origin() (cima.maps.emmap.Map method) show() (cima.detection.beads_identification.BeadsFinder method) spearman_corr() (in module cima.utils.matrices_comparison) split_into_Chromosomes() (cima.segments.segment_info.Segment method) split_into_Clusters() (cima.segments.segment_info_xyz.SegmentXYZ method) split_into_cycle() (cima.segments.segment_info.Segment method) split_into_frames_chunk() (cima.segments.segment_info.Segment method) split_into_time() (cima.segments.segment_info_xyz.SegmentXYZ method) splitByValue() (cima.segments.segment_info_xyz.SegmentXYZ method) SR_ConvexHull() (cima.segments.segment_convex.TransformConvex method) SR_ConvexHull_array() (cima.segments.segment_convex.TransformConvex method) SR_gaussian_blur() (cima.segments.segment_gaussian.TransformBlurrer static method) SRMap() (cima.segments.segment_gaussian.TransformBlurrer static method) statConvert() (in module cima.utils.stats_function) std() (cima.maps.emmap.Map method) StructureBlurrer (class in cima.maps.structure_blurrer)

T

threshold_map() (cima.maps.emmap.Map method) ThresholdClusterFilter (class in cima.detection.clusters) times() (cima.utils.vector.Vector method) TimesIDs() (cima.segments.segment_info_xyz.SegmentXYZ method) to_atom() (cima.utils.vector.Vector method)

torsion() (in module cima.utils.vector) TransformBlurrer (class in cima.segments.segment_gaussian) TransformConvex (class in cima.segments.segment_convex) transformed_segment (cima.detection.clusters.ThresholdClusterFilter attribute) translate() (cima.maps.emmap.Map method) (cima.utils.vector.Vector method)

U

unit() (cima.utils.vector.Vector method)

update_header() (cima.maps.emmap.Map method) upperDiagCsr() (cima.utils.matrices_comparison.SCCComputer method)

V

varVstran() (cima.utils.matrices_comparison.SCCComputer method) Vector (class in cima.utils.vector)

vectorise_point() (cima.maps.emmap.Map method) VQ() (in module cima.maps.vq)

W

welch_ttest() (in module cima.utils.stats_function) where_retain (cima.detection.clusters.ThresholdClusterFilter attribute) write_CSV_file() (cima.parsers.parser_csv.CSVParser static method)

write_to_MRC_file() (cima.maps.emmap.Map method) writeCOM_toPDB() (in module cima.utils.write_pdb) writeMRCs() (cima.detection.clusters.ThresholdClusterFilter method) writeToH5SingleDataset() (cima.parsers.parser_h5py.h5pyParser static method)

X

x_origin() (cima.maps.emmap.Map method)

x_size() (cima.maps.emmap.Map method)

Y

y_origin() (cima.maps.emmap.Map method)

y_size() (cima.maps.emmap.Map method)

Z

z_origin() (cima.maps.emmap.Map method)

z_size() (cima.maps.emmap.Map method)