Index

_

__getitem__() (janelia_core.fileio.data_handlers.NDArrayHandler method) (janelia_core.ml.datasets.TimeSeriesBatch method) (janelia_core.ml.datasets.TimeSeriesDataset method) (janelia_core.visualization.custom_color_maps.MultiParamCMap method) __getstate__() (janelia_core.fileio.data_handlers.NDArrayHandler method) __len__() (janelia_core.ml.datasets.TimeSeriesBatch method) (janelia_core.ml.datasets.TimeSeriesDataset method) __setitem__() (janelia_core.fileio.data_handlers.NDArrayHandler method) __str__() (janelia_core.ml.torch_distributions.ColumnMeanClusterPenalizer method) (janelia_core.ml.torch_parameter_penalizers.ClusterPenalizer method) (janelia_core.ml.torch_parameter_penalizers.ParameterPenalizer method) (janelia_core.ml.torch_parameter_penalizers.ScalarPenalizer method) (janelia_core.ml.torch_parameter_penalizers.TargetLengthPenalizer method)

_f() (janelia_core.ml.generation.BumpFcnGenerator method) _gen_roi_image() (janelia_core.visualization.roi_exploration.ROIViewer method) _get_bin() (janelia_core.stats.histogram.HistogramFilter method) _percentile_filter_arg_unpack() (in module janelia_core.dataprocessing.baseline) _x_to_idx() (janelia_core.ml.extra_torch_modules.SumOfTiledHyperCubeBasisFcns method)

A

add_value() (janelia_core.stats.histogram.HistogramFilter method) aligned_mean() (in module janelia_core.stats.averages) all_pairs_perm_tests() (in module janelia_core.stats.permutation_tests) alpha_composite() (in module janelia_core.visualization.image_generation)

alpha_overlay() (in module janelia_core.visualization.utils) append_ts() (in module janelia_core.utils.data_saving) apply_2d_dipy_affine_transform() (in module janelia_core.registration.registration) apply_bonferroni() (in module janelia_core.stats.multiple_comparisons) apply_by() (in module janelia_core.stats.multiple_comparisons)

B

basic_perm_test() (in module janelia_core.stats.permutation_tests) BasicExp (class in janelia_core.ml.extra_torch_modules) Bias (class in janelia_core.ml.extra_torch_modules) BiasAndPositiveScale (class in janelia_core.ml.extra_torch_modules) BiasAndScale (class in janelia_core.ml.extra_torch_modules) bound() (in module janelia_core.math.basic_functions) (janelia_core.ml.extra_torch_modules.PWLNNFcn method) (janelia_core.ml.wandering_modules.BumpFcn method) (janelia_core.ml.wandering_modules.SlowSumOfBumpFcns method) (janelia_core.ml.wandering_modules.SumOfBumpFcns method) (janelia_core.ml.wandering_modules.WanderingModule method)

bounding_box() (janelia_core.dataprocessing.roi.ROI method) BumpFcn (class in janelia_core.ml.wandering_modules) BumpFcnGenerator (class in janelia_core.ml.generation)

C

calc_dataset_ref_image() (in module janelia_core.registration.registration) calculate_causal_percentile_baseline() (in module janelia_core.dataprocessing.baseline) calculate_causal_percentile_baselines() (in module janelia_core.dataprocessing.baseline) cat_time_series_batches() (in module janelia_core.ml.datasets) center_of_mass() (janelia_core.dataprocessing.roi.ROI method) check_point() (janelia_core.ml.torch_distributions.ColumnMeanClusterPenalizer method) (janelia_core.ml.torch_distributions.DistributionPenalizer method) (janelia_core.ml.torch_parameter_penalizers.ClusterPenalizer method) (janelia_core.ml.torch_parameter_penalizers.ParameterPenalizer method) (janelia_core.ml.torch_parameter_penalizers.ScalarPenalizer method) (janelia_core.ml.torch_parameter_penalizers.TargetLengthPenalizer method) clone() (janelia_core.ml.torch_parameter_penalizers.ClusterPenalizer method) (janelia_core.ml.torch_parameter_penalizers.ParameterPenalizer method) (janelia_core.ml.torch_parameter_penalizers.ScalarPenalizer method) (janelia_core.ml.torch_parameter_penalizers.TargetLengthPenalizer method) ClusterPenalizer (class in janelia_core.ml.torch_parameter_penalizers) cmp_n_mats() (in module janelia_core.visualization.matrix_visualization) colorized_tbl() (in module janelia_core.visualization.matrix_visualization) ColumnMeanClusterPenalizer (class in janelia_core.ml.torch_distributions) comb_movies() (in module janelia_core.visualization.volume_visualization)

combine_slices() (in module janelia_core.math.basic_functions) compare_models() (janelia_core.ml.reduced_rank_models.RRLinearModel static method) CondBernoulliDistribution (class in janelia_core.ml.torch_distributions) CondFoldedNormalDistribution (class in janelia_core.ml.torch_distributions) CondGammaDistribution (class in janelia_core.ml.torch_distributions) CondGaussianDistribution (class in janelia_core.ml.torch_distributions) CondGaussianMatrixProductDistribution (class in janelia_core.ml.torch_distributions) CondMatrixHypercubePrior (class in janelia_core.ml.torch_distributions) CondMatrixProductDistribution (class in janelia_core.ml.torch_distributions) CondSpikeSlabDistribution (class in janelia_core.ml.torch_distributions) CondVAEDistribution (class in janelia_core.ml.torch_distributions) ConstantBoundedFcn (class in janelia_core.ml.extra_torch_modules) ConstantRealFcn (class in janelia_core.ml.extra_torch_modules) copy_and_delay() (in module janelia_core.math.basic_functions) copy_state_from() (janelia_core.ml.torch_parameter_penalizers.ClusterPenalizer method) (janelia_core.ml.torch_parameter_penalizers.ParameterPenalizer method) (janelia_core.ml.torch_parameter_penalizers.ScalarPenalizer method) (janelia_core.ml.torch_parameter_penalizers.TargetLengthPenalizer method) corr() (in module janelia_core.stats.regression) create_morphsnakes_brain_mask() (in module janelia_core.dataprocessing.image_stats) create_threshold_brain_mask() (in module janelia_core.dataprocessing.image_stats)

D

DataSet (class in janelia_core.dataprocessing.dataset) DenseLayer (class in janelia_core.ml.extra_torch_modules) DenseLNLNet (class in janelia_core.ml.extra_torch_modules) dict_find() (in module janelia_core.utils.searching)

DistributionPenalizer (class in janelia_core.ml.torch_distributions) divide_into_nearly_equal_parts() (in module janelia_core.math.basic_functions) down_sample_ephys_vls() (in module janelia_core.dataprocessing.ahrens_lab) down_select_rois() (janelia_core.dataprocessing.dataset.ROIDataset method)

E

efficient_get_item() (janelia_core.ml.datasets.TimeSeriesBatch method) ElementWiseTanh (class in janelia_core.ml.extra_torch_modules) enforce_constant_clims() (in module janelia_core.visualization.utils) estimate_translation() (in module janelia_core.registration.registration)

Exp (class in janelia_core.ml.extra_torch_modules) extents() (janelia_core.dataprocessing.roi.ROI method) extract_rois() (in module janelia_core.cell_extraction.roi) (janelia_core.dataprocessing.dataset.ROIDataset method)

F

find_binary_runs() (in module janelia_core.math.basic_functions) find_camera_triggers_in_ephys() (in module janelia_core.dataprocessing.ahrens_lab) find_disjoint_intervals() (in module janelia_core.math.basic_functions) find_first_after() (in module janelia_core.math.basic_functions) find_first_before() (in module janelia_core.math.basic_functions) find_images() (in module janelia_core.fileio.exp_reader) FirstAndSecondOrderFcn (class in janelia_core.ml.extra_torch_modules) fisher_lda() (in module janelia_core.ml.lda) fit() (janelia_core.ml.reduced_rank_models.RRLinearModel method) FixedOffsetAbs (class in janelia_core.ml.extra_torch_modules) FixedOffsetExp (class in janelia_core.ml.extra_torch_modules) FixedOffsetTanh (class in janelia_core.ml.extra_torch_modules) flip_weight_signs() (janelia_core.ml.reduced_rank_models.RRLinearModel method) form_compact_sample() (janelia_core.ml.torch_distributions.CondBernoulliDistribution method) (janelia_core.ml.torch_distributions.CondFoldedNormalDistribution method) (janelia_core.ml.torch_distributions.CondGammaDistribution method) (janelia_core.ml.torch_distributions.CondGaussianDistribution method) (janelia_core.ml.torch_distributions.CondMatrixProductDistribution method) (janelia_core.ml.torch_distributions.CondSpikeSlabDistribution method) (janelia_core.ml.torch_distributions.CondVAEDistribution method) form_composite_rois() (janelia_core.dataprocessing.dataset.ROIDataset method) form_standard_sample() (janelia_core.ml.torch_distributions.CondBernoulliDistribution method) (janelia_core.ml.torch_distributions.CondFoldedNormalDistribution method) (janelia_core.ml.torch_distributions.CondGammaDistribution method) (janelia_core.ml.torch_distributions.CondGaussianDistribution method) (janelia_core.ml.torch_distributions.CondMatrixProductDistribution method) (janelia_core.ml.torch_distributions.CondSpikeSlabDistribution method) (janelia_core.ml.torch_distributions.CondVAEDistribution method) format_and_check_learning_rates() (in module janelia_core.ml.utils) FormMatrixByCols (class in janelia_core.ml.extra_torch_modules) forward() (janelia_core.ml.extra_torch_modules.BasicExp method) (janelia_core.ml.extra_torch_modules.Bias method) (janelia_core.ml.extra_torch_modules.BiasAndPositiveScale method) (janelia_core.ml.extra_torch_modules.BiasAndScale method) (janelia_core.ml.extra_torch_modules.ConstantBoundedFcn method) (janelia_core.ml.extra_torch_modules.ConstantRealFcn method) (janelia_core.ml.extra_torch_modules.DenseLayer method) (janelia_core.ml.extra_torch_modules.DenseLNLNet method) (janelia_core.ml.extra_torch_modules.ElementWiseTanh method) (janelia_core.ml.extra_torch_modules.Exp method) (janelia_core.ml.extra_torch_modules.FirstAndSecondOrderFcn method) (janelia_core.ml.extra_torch_modules.FixedOffsetAbs method) (janelia_core.ml.extra_torch_modules.FixedOffsetExp method) (janelia_core.ml.extra_torch_modules.FixedOffsetTanh method) (janelia_core.ml.extra_torch_modules.FormMatrixByCols method) (janelia_core.ml.extra_torch_modules.IndSmpConstantBoundedFcn method) (janelia_core.ml.extra_torch_modules.IndSmpConstantRealFcn method) (janelia_core.ml.extra_torch_modules.LogGaussianBumpFcn method) (janelia_core.ml.extra_torch_modules.PWLNNFcn method) (janelia_core.ml.extra_torch_modules.QuadSurf method) (janelia_core.ml.extra_torch_modules.RBF method) (janelia_core.ml.extra_torch_modules.Relu method) (janelia_core.ml.extra_torch_modules.SCC method) (janelia_core.ml.extra_torch_modules.SumAlongDim method) (janelia_core.ml.extra_torch_modules.SumOfRelus method) (janelia_core.ml.extra_torch_modules.SumOfTiledHyperCubeBasisFcns method) (janelia_core.ml.extra_torch_modules.SwissRole method) (janelia_core.ml.extra_torch_modules.Tanh method) (janelia_core.ml.extra_torch_modules.Unsqueeze method) (janelia_core.ml.reduced_rank_models.RRExpModel method) (janelia_core.ml.reduced_rank_models.RRLinearModel method) (janelia_core.ml.reduced_rank_models.RRReluModel method) (janelia_core.ml.reduced_rank_models.RRSigmoidModel method) (janelia_core.ml.torch_distributions.CondBernoulliDistribution method) (janelia_core.ml.torch_distributions.CondFoldedNormalDistribution method) (janelia_core.ml.torch_distributions.CondGammaDistribution method) (janelia_core.ml.torch_distributions.CondGaussianDistribution method) (janelia_core.ml.torch_distributions.CondMatrixProductDistribution method) (janelia_core.ml.torch_distributions.CondSpikeSlabDistribution method) (janelia_core.ml.torch_distributions.CondVAEDistribution method) (janelia_core.ml.torch_distributions.MatrixFoldedNormalProductDistribution method) (janelia_core.ml.wandering_modules.BumpFcn method) (janelia_core.ml.wandering_modules.SlowSumOfBumpFcns method) (janelia_core.ml.wandering_modules.SumOfBumpFcns method)

from_array() (janelia_core.dataprocessing.roi.ROI class method) from_dict() (janelia_core.dataprocessing.dataset.DataSet class method) (janelia_core.dataprocessing.dataset.PointDataset class method) (janelia_core.dataprocessing.dataset.ROIDataset class method) (janelia_core.dataprocessing.point.Point class method) (janelia_core.dataprocessing.roi.ROI class method) (janelia_core.visualization.custom_color_maps.MultiParamCMap class method) from_state_dict() (janelia_core.ml.reduced_rank_models.RRExpModel class method) (janelia_core.ml.reduced_rank_models.RRLinearModel class method) (janelia_core.ml.reduced_rank_models.RRReluModel class method) (janelia_core.ml.reduced_rank_models.RRSigmoidModel class method)

G

gen_columns_mean_cluster_penalizer() (in module janelia_core.ml.torch_distributions) gen_composite_roi_vol() (in module janelia_core.visualization.volume_visualization) generate() (janelia_core.ml.generation.BumpFcnGenerator method) (janelia_core.ml.reduced_rank_models.RRLinearModel method) generate_2d_fcn_image() (in module janelia_core.visualization.image_generation) generate_balanced_folds() (in module janelia_core.ml.cv) generate_binary_color_rgba_image() (in module janelia_core.visualization.image_generation) generate_dot_image() (in module janelia_core.visualization.image_generation) generate_dot_image_3d() (in module janelia_core.visualization.image_generation) generate_hypergrid_pts() (in module janelia_core.math.basic_functions) generate_image_from_fcn() (in module janelia_core.visualization.image_generation) generate_mean_dot_image() (in module janelia_core.visualization.image_generation) generate_normalized_rgb_cmap() (in module janelia_core.visualization.custom_color_maps) generate_random_model() (janelia_core.ml.reduced_rank_models.RRExpModel method) (janelia_core.ml.reduced_rank_models.RRLinearModel method) (janelia_core.ml.reduced_rank_models.RRReluModel method) (janelia_core.ml.reduced_rank_models.RRSigmoidModel method) generate_two_param_hsv_map() (in module janelia_core.visualization.custom_color_maps) generate_two_param_norm_map() (in module janelia_core.visualization.custom_color_maps) get_2d_confidence_ellipse() (in module janelia_core.stats.utils) get_bin_starting_edges() (janelia_core.stats.histogram.HistogramFilter method)

get_current_memory_usage() (in module janelia_core.utils.memory_management) get_image_data() (in module janelia_core.dataprocessing.utils) get_immediate_subfolders() (in module janelia_core.utils.file_system) get_marked_params() (janelia_core.ml.torch_distributions.ColumnMeanClusterPenalizer method) (janelia_core.ml.torch_distributions.DistributionPenalizer method) (janelia_core.ml.torch_parameter_penalizers.ClusterPenalizer method) (janelia_core.ml.torch_parameter_penalizers.ParameterPenalizer method) (janelia_core.ml.torch_parameter_penalizers.ScalarPenalizer method) (janelia_core.ml.torch_parameter_penalizers.TargetLengthPenalizer method) get_processed_image_data() (in module janelia_core.dataprocessing.utils) get_reg_image_data() (in module janelia_core.dataprocessing.utils) get_rois_center_of_mass() (janelia_core.dataprocessing.dataset.ROIDataset method) get_valid_translated_image_window() (in module janelia_core.registration.registration) GroupCondMatrixHypercubePrior (class in janelia_core.ml.torch_distributions) grouped_linear_regression_acm_linear_restriction_stats() (in module janelia_core.stats.regression) grouped_linear_regression_acm_stats() (in module janelia_core.stats.regression) grouped_linear_regression_boot_strap() (in module janelia_core.stats.regression) grouped_linear_regression_boot_strap_stats() (in module janelia_core.stats.regression) grouped_linear_regression_ols_estimator() (in module janelia_core.stats.regression) grouped_linear_regression_wild_bootstrap() (in module janelia_core.stats.regression) grouped_linear_regression_within_estimator() (in module janelia_core.stats.regression) GroupedStackedImageVisualizer (class in janelia_core.visualization.image_visualization)

H

has_ts_data() (janelia_core.dataprocessing.dataset.DataSet method)

HDF5_TYPES (in module janelia_core.utils.data_saving) HistogramFilter (class in janelia_core.stats.histogram)

I

identify_rois_in_brain_mask() (in module janelia_core.dataprocessing.image_stats) identify_small_rois() (in module janelia_core.dataprocessing.image_stats) IMG_SMP_NUM_FILE_NAME_REG_EXP (in module janelia_core.fileio.exp_reader) increase_std() (janelia_core.ml.torch_distributions.CondMatrixHypercubePrior method) IndSmpConstantBoundedFcn (class in janelia_core.ml.extra_torch_modules) IndSmpConstantRealFcn (class in janelia_core.ml.extra_torch_modules) infer_latents() (janelia_core.ml.reduced_rank_models.RRLinearModel method) init_ui() (janelia_core.visualization.image_visualization.GroupedStackedImageVisualizer method) (janelia_core.visualization.roi_exploration.MultiPlaneROIViewer method) (janelia_core.visualization.roi_exploration.ROIViewer method) (janelia_core.visualization.roi_exploration.StaticROIViewer method) (janelia_core.visualization.roi_exploration.TimeLine method)

init_weights() (janelia_core.ml.reduced_rank_models.RRExpModel method) (janelia_core.ml.reduced_rank_models.RRLinearModel method) (janelia_core.ml.reduced_rank_models.RRReluModel method) (janelia_core.ml.reduced_rank_models.RRSigmoidModel method) initialize() (janelia_core.ml.torch_distributions.MatrixGaussianProductDistribution method) injest() (janelia_core.stats.bootstrap.OnlineNonZeroPVlCalculator method) int_to_arb_base() (in module janelia_core.math.basic_functions) intersect_plane() (janelia_core.dataprocessing.roi.ROI method) is_fully_specified_slice() (in module janelia_core.math.basic_functions) is_simple_slice() (in module janelia_core.math.basic_functions) is_standard_slice() (in module janelia_core.math.basic_functions)

J

janelia_core module janelia_core.cell_extraction module janelia_core.cell_extraction.roi module janelia_core.dataprocessing module janelia_core.dataprocessing.ahrens_lab module janelia_core.dataprocessing.baseline module janelia_core.dataprocessing.data_handling module janelia_core.dataprocessing.dataset module janelia_core.dataprocessing.image_stats module janelia_core.dataprocessing.point module janelia_core.dataprocessing.roi module janelia_core.dataprocessing.utils module janelia_core.fileio module janelia_core.fileio.ahrens_lab module janelia_core.fileio.data_handlers module janelia_core.fileio.exp_reader module janelia_core.math module janelia_core.math.basic_functions module janelia_core.ml module janelia_core.ml.cv module janelia_core.ml.datasets module janelia_core.ml.extra_torch_functions module janelia_core.ml.extra_torch_modules module janelia_core.ml.fitting module janelia_core.ml.generation module janelia_core.ml.lda module janelia_core.ml.reduced_rank_models module janelia_core.ml.torch_distributions module

janelia_core.ml.torch_parameter_penalizers module janelia_core.ml.utils module janelia_core.ml.wandering_modules module janelia_core.registration module janelia_core.registration.registration module janelia_core.stats module janelia_core.stats.averages module janelia_core.stats.bootstrap module janelia_core.stats.histogram module janelia_core.stats.multiple_comparisons module janelia_core.stats.permutation_tests module janelia_core.stats.regression module janelia_core.stats.utils module janelia_core.utils module janelia_core.utils.data_saving module janelia_core.utils.file_system module janelia_core.utils.memory_management module janelia_core.utils.searching module janelia_core.visualization module janelia_core.visualization.custom_color_maps module janelia_core.visualization.exp_viewing module janelia_core.visualization.image_generation module janelia_core.visualization.image_visualization module janelia_core.visualization.matrix_visualization module janelia_core.visualization.roi_exploration module janelia_core.visualization.signal_visualization module janelia_core.visualization.utils module janelia_core.visualization.volume_visualization module

K

keyPressEvent() (janelia_core.visualization.exp_viewing.KeyPressWindow method) (janelia_core.visualization.roi_exploration.ROIViewer method) (janelia_core.visualization.roi_exploration.StaticROIViewer method) KeyPressWindow (class in janelia_core.visualization.exp_viewing) kl() (janelia_core.ml.torch_distributions.CondGammaDistribution method) (janelia_core.ml.torch_distributions.CondGaussianDistribution method) (janelia_core.ml.torch_distributions.CondGaussianMatrixProductDistribution method) (janelia_core.ml.torch_distributions.CondMatrixProductDistribution method) (janelia_core.ml.torch_distributions.CondVAEDistribution method)

knn_do() (in module janelia_core.ml.extra_torch_functions) knn_mc() (in module janelia_core.ml.extra_torch_functions)

L

l_th() (in module janelia_core.math.basic_functions) latent_rep() (janelia_core.ml.reduced_rank_models.RRExpModel method) linear_regression_ols_estimator() (in module janelia_core.stats.regression) list_all_voxel_inds() (janelia_core.dataprocessing.roi.ROI method) list_all_weights() (janelia_core.dataprocessing.roi.ROI method) list_grid_pts() (in module janelia_core.math.basic_functions) list_param_keys() (janelia_core.ml.torch_distributions.ColumnMeanClusterPenalizer method) (janelia_core.ml.torch_distributions.DistributionPenalizer method) (janelia_core.ml.torch_parameter_penalizers.ClusterPenalizer method) (janelia_core.ml.torch_parameter_penalizers.ParameterPenalizer method) (janelia_core.ml.torch_parameter_penalizers.ScalarPenalizer method) (janelia_core.ml.torch_parameter_penalizers.TargetLengthPenalizer method) list_torch_devices() (in module janelia_core.ml.utils)

load_data() (janelia_core.fileio.data_handlers.NDArrayHandler method) load_structured_hdf5() (in module janelia_core.utils.data_saving) LOG_2 (in module janelia_core.ml.extra_torch_functions) log_cosh() (in module janelia_core.ml.extra_torch_functions) log_prob() (janelia_core.ml.torch_distributions.CondBernoulliDistribution method) (janelia_core.ml.torch_distributions.CondFoldedNormalDistribution method) (janelia_core.ml.torch_distributions.CondGammaDistribution method) (janelia_core.ml.torch_distributions.CondGaussianDistribution method) (janelia_core.ml.torch_distributions.CondMatrixProductDistribution method) (janelia_core.ml.torch_distributions.CondSpikeSlabDistribution method) (janelia_core.ml.torch_distributions.CondVAEDistribution method) (janelia_core.ml.torch_distributions.MatrixFoldedNormalProductDistribution method) LogGaussianBumpFcn (class in janelia_core.ml.extra_torch_modules)

M

make_purple_green_c_map() (in module janelia_core.visualization.custom_color_maps) make_red_green_c_map() (in module janelia_core.visualization.custom_color_maps) make_rgb_three_ch_z_plane_movie() (in module janelia_core.visualization.volume_visualization) make_rgb_z_plane_movie() (in module janelia_core.visualization.volume_visualization) make_z_plane_movie() (in module janelia_core.visualization.volume_visualization) match_torch_module() (in module janelia_core.ml.fitting) MatrixFoldedNormalProductDistribution (class in janelia_core.ml.torch_distributions) MatrixGammaProductDistribution (class in janelia_core.ml.torch_distributions) MatrixGaussianProductDistribution (class in janelia_core.ml.torch_distributions) max_project_pts() (in module janelia_core.visualization.image_generation) median_filter_2d_dipy_affine_transforms() (in module janelia_core.registration.registration) mode() (janelia_core.ml.torch_distributions.CondGammaDistribution method) module janelia_core janelia_core.cell_extraction janelia_core.cell_extraction.roi janelia_core.dataprocessing janelia_core.dataprocessing.ahrens_lab janelia_core.dataprocessing.baseline janelia_core.dataprocessing.data_handling janelia_core.dataprocessing.dataset janelia_core.dataprocessing.image_stats janelia_core.dataprocessing.point janelia_core.dataprocessing.roi janelia_core.dataprocessing.utils janelia_core.fileio janelia_core.fileio.ahrens_lab janelia_core.fileio.data_handlers janelia_core.fileio.exp_reader janelia_core.math janelia_core.math.basic_functions janelia_core.ml janelia_core.ml.cv janelia_core.ml.datasets janelia_core.ml.extra_torch_functions janelia_core.ml.extra_torch_modules janelia_core.ml.fitting janelia_core.ml.generation janelia_core.ml.lda janelia_core.ml.reduced_rank_models janelia_core.ml.torch_distributions janelia_core.ml.torch_parameter_penalizers janelia_core.ml.utils janelia_core.ml.wandering_modules janelia_core.registration janelia_core.registration.registration janelia_core.stats janelia_core.stats.averages janelia_core.stats.bootstrap janelia_core.stats.histogram janelia_core.stats.multiple_comparisons janelia_core.stats.permutation_tests janelia_core.stats.regression janelia_core.stats.utils janelia_core.utils janelia_core.utils.data_saving janelia_core.utils.file_system janelia_core.utils.memory_management janelia_core.utils.searching janelia_core.visualization janelia_core.visualization.custom_color_maps janelia_core.visualization.exp_viewing janelia_core.visualization.image_generation janelia_core.visualization.image_visualization janelia_core.visualization.matrix_visualization janelia_core.visualization.roi_exploration janelia_core.visualization.signal_visualization janelia_core.visualization.utils janelia_core.visualization.volume_visualization

MultiParamCMap (class in janelia_core.visualization.custom_color_maps) MultiPlaneROIViewer (class in janelia_core.visualization.roi_exploration)

N

n_voxels() (janelia_core.dataprocessing.roi.ROI method) naive_regression() (in module janelia_core.stats.regression) nan_matrix() (in module janelia_core.math.basic_functions)

NDArrayHandler (class in janelia_core.fileio.data_handlers) neg_log_likelihood() (janelia_core.ml.reduced_rank_models.RRLinearModel method) normalized_r_squared() (in module janelia_core.stats.regression)

O

OnlineNonZeroPVlCalculator (class in janelia_core.stats.bootstrap)

optimal_orthonormal_transform() (in module janelia_core.math.basic_functions) OptionalTensor (in module janelia_core.ml.extra_torch_modules)

P

p_vls() (janelia_core.stats.bootstrap.OnlineNonZeroPVlCalculator method) paired_grouped_perm_test() (in module janelia_core.stats.permutation_tests) parameter_combinations() (in module janelia_core.ml.cv) ParameterPenalizer (class in janelia_core.ml.torch_parameter_penalizers) penalize() (janelia_core.ml.torch_distributions.ColumnMeanClusterPenalizer method) (janelia_core.ml.torch_distributions.DistributionPenalizer method) penalize_and_backwards() (janelia_core.ml.torch_parameter_penalizers.ClusterPenalizer method) (janelia_core.ml.torch_parameter_penalizers.ParameterPenalizer method) (janelia_core.ml.torch_parameter_penalizers.ScalarPenalizer method) (janelia_core.ml.torch_parameter_penalizers.TargetLengthPenalizer method) (janelia_core.ml.torch_parameter_penalizers.UnsignedClusterPenalizer method) (janelia_core.ml.torch_parameter_penalizers.UnsignedScalarPenalizer method) percentile() (janelia_core.stats.histogram.HistogramFilter method)

percentile_filter_1d() (in module janelia_core.dataprocessing.baseline) percentile_filter_multi_d() (in module janelia_core.dataprocessing.baseline) pert_grads() (janelia_core.ml.wandering_modules.BumpFcn method) (janelia_core.ml.wandering_modules.SlowSumOfBumpFcns method) (janelia_core.ml.wandering_modules.SumOfBumpFcns method) (janelia_core.ml.wandering_modules.WanderingModule method) pin_memory() (janelia_core.ml.datasets.TimeSeriesBatch method) plot_segmented_signal() (in module janelia_core.visualization.signal_visualization) Point (class in janelia_core.dataprocessing.point) PointDataset (class in janelia_core.dataprocessing.dataset) premultiplied_rgba_to_standard() (in module janelia_core.visualization.image_generation) process_key_press() (janelia_core.visualization.roi_exploration.StaticROIViewer method) pts_in_arc() (in module janelia_core.math.basic_functions) PWLNNFcn (class in janelia_core.ml.extra_torch_modules)

Q

QuadSurf (class in janelia_core.ml.extra_torch_modules)

R

r_params() (janelia_core.ml.torch_distributions.CondBernoulliDistribution method) (janelia_core.ml.torch_distributions.CondFoldedNormalDistribution method) (janelia_core.ml.torch_distributions.CondGammaDistribution method) (janelia_core.ml.torch_distributions.CondGaussianDistribution method) (janelia_core.ml.torch_distributions.CondMatrixProductDistribution method) (janelia_core.ml.torch_distributions.CondSpikeSlabDistribution method) (janelia_core.ml.torch_distributions.CondVAEDistribution method) r_squared() (in module janelia_core.stats.regression) RBF (class in janelia_core.ml.extra_torch_modules) read_ephys_data() (in module janelia_core.fileio.ahrens_lab) read_exp() (in module janelia_core.fileio.ahrens_lab) read_imaging_metadata() (in module janelia_core.fileio.exp_reader) read_img_file() (in module janelia_core.fileio.exp_reader) read_raw_ephys_data() (in module janelia_core.fileio.ahrens_lab)

read_separated_exp() (in module janelia_core.fileio.ahrens_lab) read_stack_freq() (in module janelia_core.fileio.ahrens_lab) register_dataset_images() (in module janelia_core.registration.registration) Relu (class in janelia_core.ml.extra_torch_modules) remove_value() (janelia_core.stats.histogram.HistogramFilter method) reset() (janelia_core.stats.histogram.HistogramFilter method) rgb_3d_max_project() (in module janelia_core.visualization.image_generation) ROI (class in janelia_core.dataprocessing.roi) roi_clrs (in module janelia_core.visualization.roi_exploration) ROIDataset (class in janelia_core.dataprocessing.dataset) ROIViewer (class in janelia_core.visualization.roi_exploration) RRExpModel (class in janelia_core.ml.reduced_rank_models) RRLinearModel (class in janelia_core.ml.reduced_rank_models) RRReluModel (class in janelia_core.ml.reduced_rank_models) RRSigmoidModel (class in janelia_core.ml.reduced_rank_models)

S

s_params() (janelia_core.ml.torch_distributions.CondBernoulliDistribution method) (janelia_core.ml.torch_distributions.CondFoldedNormalDistribution method) (janelia_core.ml.torch_distributions.CondGammaDistribution method) (janelia_core.ml.torch_distributions.CondGaussianDistribution method) (janelia_core.ml.torch_distributions.CondMatrixProductDistribution method) (janelia_core.ml.torch_distributions.CondSpikeSlabDistribution method) (janelia_core.ml.torch_distributions.CondVAEDistribution method) sample() (janelia_core.ml.torch_distributions.CondBernoulliDistribution method) (janelia_core.ml.torch_distributions.CondFoldedNormalDistribution method) (janelia_core.ml.torch_distributions.CondGammaDistribution method) (janelia_core.ml.torch_distributions.CondGaussianDistribution method) (janelia_core.ml.torch_distributions.CondMatrixProductDistribution method) (janelia_core.ml.torch_distributions.CondSpikeSlabDistribution method) (janelia_core.ml.torch_distributions.CondVAEDistribution method) (janelia_core.ml.torch_distributions.MatrixFoldedNormalProductDistribution method) sample_to() (janelia_core.ml.torch_distributions.CondFoldedNormalDistribution method) (janelia_core.ml.torch_distributions.CondGammaDistribution method) (janelia_core.ml.torch_distributions.CondGaussianDistribution method) (janelia_core.ml.torch_distributions.CondMatrixProductDistribution method) (janelia_core.ml.torch_distributions.CondVAEDistribution method) save_data() (janelia_core.fileio.data_handlers.NDArrayHandler method) save_structured_hdf5() (in module janelia_core.utils.data_saving) scalar_3d_max_project() (in module janelia_core.visualization.image_generation) ScalarPenalizer (class in janelia_core.ml.torch_parameter_penalizers) scale_grads() (janelia_core.ml.reduced_rank_models.RRLinearModel method) SCC (class in janelia_core.ml.extra_torch_modules) select_subslice() (in module janelia_core.math.basic_functions) select_time_range() (janelia_core.dataprocessing.dataset.DataSet method) select_ts_data() (janelia_core.dataprocessing.dataset.DataSet method) set_data() (janelia_core.fileio.data_handlers.NDArrayHandler method) set_mn() (janelia_core.ml.torch_distributions.CondMatrixHypercubePrior method)

set_plane() (janelia_core.visualization.roi_exploration.StaticROIViewer method) set_std() (janelia_core.ml.torch_distributions.CondMatrixHypercubePrior method) set_value() (janelia_core.ml.extra_torch_modules.ConstantBoundedFcn method) (janelia_core.ml.extra_torch_modules.IndSmpConstantBoundedFcn method) (janelia_core.ml.extra_torch_modules.IndSmpConstantRealFcn method) (janelia_core.visualization.roi_exploration.ROIViewer method) set_vl() (janelia_core.ml.extra_torch_modules.ConstantRealFcn method) sigKeyPress (janelia_core.visualization.exp_viewing.KeyPressWindow attribute) (janelia_core.visualization.roi_exploration.ROIViewer attribute) (janelia_core.visualization.roi_exploration.StaticROIViewer attribute) signed_max_proj() (in module janelia_core.visualization.volume_visualization) signed_max_project() (in module janelia_core.visualization.image_generation) slice_contains() (in module janelia_core.math.basic_functions) slice_roi() (janelia_core.dataprocessing.roi.ROI method) SlowSumOfBumpFcns (class in janelia_core.ml.wandering_modules) split_images() (in module janelia_core.dataprocessing.data_handling) STACK_FREQ_EXP_DURATION_LINE (in module janelia_core.fileio.ahrens_lab) STACK_FREQ_N_IMAGES_LINE (in module janelia_core.fileio.ahrens_lab) STACK_FREQ_STACK_FREQ_LINE (in module janelia_core.fileio.ahrens_lab) standard_rgba_to_premultiplied() (in module janelia_core.visualization.image_generation) standardize() (janelia_core.ml.reduced_rank_models.RRLinearModel method) (janelia_core.ml.reduced_rank_models.RRSigmoidModel method) StaticROIViewer (class in janelia_core.visualization.roi_exploration) std() (janelia_core.ml.torch_distributions.CondGammaDistribution method) std_through_time() (in module janelia_core.dataprocessing.image_stats) SumAlongDim (class in janelia_core.ml.extra_torch_modules) summarize_memory_stats() (in module janelia_core.ml.utils) SumOfBumpFcns (class in janelia_core.ml.wandering_modules) SumOfRelus (class in janelia_core.ml.extra_torch_modules) SumOfTiledHyperCubeBasisFcns (class in janelia_core.ml.extra_torch_modules) SwissRole (class in janelia_core.ml.extra_torch_modules)

T

Tanh (class in janelia_core.ml.extra_torch_modules) TargetLengthPenalizer (class in janelia_core.ml.torch_parameter_penalizers) time_dragged (janelia_core.visualization.roi_exploration.TimeLine attribute) TimeLine (class in janelia_core.visualization.roi_exploration) TimeSeriesBatch (class in janelia_core.ml.datasets) TimeSeriesDataset (class in janelia_core.ml.datasets) to() (janelia_core.ml.datasets.TimeSeriesBatch method)

to_dict() (janelia_core.dataprocessing.dataset.DataSet method) (janelia_core.dataprocessing.dataset.PointDataset method) (janelia_core.dataprocessing.dataset.ROIDataset method) (janelia_core.dataprocessing.point.Point method) (janelia_core.dataprocessing.roi.ROI method) (janelia_core.visualization.custom_color_maps.MultiParamCMap method) torch_devices_memory_usage() (in module janelia_core.ml.utils) torch_mod_to_fcn() (in module janelia_core.ml.utils)

U

u_th() (in module janelia_core.math.basic_functions) UnsignedClusterPenalizer (class in janelia_core.ml.torch_parameter_penalizers)

UnsignedScalarPenalizer (class in janelia_core.ml.torch_parameter_penalizers) Unsqueeze (class in janelia_core.ml.extra_torch_modules) update_image_folder() (janelia_core.dataprocessing.dataset.DataSet static method)

V

vary_latents() (janelia_core.ml.reduced_rank_models.RRReluModel method) view_images_with_continuous_values() (in module janelia_core.visualization.exp_viewing) visualize_2d_function() (in module janelia_core.visualization.image_visualization) visualize_boot_strap_results() (in module janelia_core.stats.regression)

visualize_coefficient_stats() (in module janelia_core.stats.regression) visualize_exp() (in module janelia_core.visualization.exp_viewing) visualize_projs() (in module janelia_core.visualization.volume_visualization) visualize_rgb_max_project() (in module janelia_core.visualization.volume_visualization) visualize_two_param_map() (in module janelia_core.visualization.custom_color_maps)

W

WanderingModule (class in janelia_core.ml.wandering_modules)

write_planes_for_one_file() (in module janelia_core.dataprocessing.utils) write_planes_to_files() (in module janelia_core.dataprocessing.utils)