Index

A

add_singleton_axis_beginning() (in module nanshe.util.xnumpy) add_singleton_axis_end() (in module nanshe.util.xnumpy) add_singleton_axis_pos() (in module nanshe.util.xnumpy)

add_singleton_op() (in module nanshe.util.xnumpy) all_permutations_equal() (in module nanshe.util.xnumpy) array_to_matrix() (in module nanshe.util.xnumpy)

B

binary_dilation() (in module nanshe.imp.filters.masks) binary_erosion() (in module nanshe.imp.filters.masks)

binomial_1D_array_kernel() (in module nanshe.imp.filters.wavelet) binomial_1D_vigra_kernel() (in module nanshe.imp.filters.wavelet) binomial_coefficients() (in module nanshe.util.xnumpy)

C

call_multiprocessing_array_spams_trainDL() (in module nanshe.box.spams_sandbox) call_multiprocessing_queue_spams_trainDL() (in module nanshe.box.spams_sandbox) call_spams_trainDL() (in module nanshe.box.spams_sandbox) class_static_array_debug_recorder() (in module nanshe.io.hdf5.record) class_static_subgrouping_array_recorders() (in module nanshe.io.hdf5.record)

compute_mapping_matches() (in module nanshe.util.xnumpy) compute_mapping_relevance() (in module nanshe.util.xnumpy) contains() (in module nanshe.util.xnumpy) convert_tiffs() (in module nanshe.io.xtiff) create_numpy_structured_array_in_HDF5() (in module nanshe.io.hdf5.serializers)

D

data (nanshe.io.hdf5.serializers.HDF5MaskedDataset attribute) DictionaryLearningRandomDataGenerator (class in nanshe.misc.random_dictionary_learning_data) DictionaryLearningRandomDataSample (class in nanshe.misc.random_dictionary_learning_data) dims (nanshe.io.hdf5.serializers.HDF5MaskedDataset attribute)

dot_product() (in module nanshe.util.xnumpy) dot_product_L2_normalized() (in module nanshe.util.xnumpy) dot_product_normalized() (in module nanshe.util.xnumpy) dot_product_partially_normalized() (in module nanshe.util.xnumpy) dtype (nanshe.io.hdf5.serializers.HDF5MaskedDataset attribute)

E

EmptyArrayRecorder (class in nanshe.io.hdf5.record) enumerate_masks() (in module nanshe.util.xnumpy) enumerate_masks_max() (in module nanshe.util.xnumpy) estimate_f0() (in module nanshe.imp.segment) estimate_noise() (in module nanshe.imp.filters.noise) expand_arange() (in module nanshe.util.xnumpy)

expand_pathname_list() (in module nanshe.util.xglob) expand_rois() (in module nanshe.imp.segment) expand_view() (in module nanshe.util.xnumpy) extended_region_local_maxima_properties() (in module nanshe.imp.segment) ExtendedRegionProps (class in nanshe.imp.segment) extract_f0() (in module nanshe.imp.segment) extract_neurons() (in module nanshe.imp.segment)

F

fill_value (nanshe.io.hdf5.serializers.HDF5MaskedDataset attribute) filled_stringify_enumerate() (in module nanshe.util.iters) filled_stringify_numbers() (in module nanshe.util.iters) filled_stringify_xrange() (in module nanshe.util.iters)

find_offsets() (in module nanshe.imp.registration) find_relative_offsets() (in module nanshe.util.xnumpy) find_shortest_wraparound() (in module nanshe.util.xnumpy) fuse_neurons() (in module nanshe.imp.segment)

G

generate_contour() (in module nanshe.util.xnumpy) generate_dictionary() (in module nanshe.imp.segment) generate_gaussian_images() (in module nanshe.syn.data) generate_HDF5_array_recorder() (in module nanshe.io.hdf5.record) generate_hyperdisc_masks() (in module nanshe.syn.data) generate_hypersphere_masks() (in module nanshe.syn.data) generate_labeled_contours() (in module nanshe.util.xnumpy) generate_local_maxima() (in module nanshe.imp.segment) generate_local_maxima_scikit_image() (in module nanshe.imp.segment) generate_local_maxima_vigra() (in module nanshe.imp.segment) generate_neurons() (in module nanshe.learner) generate_neurons_a_block() (in module nanshe.learner) generate_neurons_blocks() (in module nanshe.learner) generate_neurons_io_handler() (in module nanshe.learner) generate_random_bound_points() (in module nanshe.syn.data) generate_unit_phase_shifts() (in module nanshe.imp.registration) get() (nanshe.io.hdf5.record.EmptyArrayRecorder method) (nanshe.io.hdf5.record.HDF5ArrayRecorder method) (nanshe.io.hdf5.record.HDF5EnumeratedArrayRecorder method)

get_empty_neuron() (in module nanshe.imp.segment) get_local_max_index_array() (nanshe.imp.segment.ExtendedRegionProps method) get_local_max_label_image() (nanshe.imp.segment.ExtendedRegionProps method) get_local_max_mask() (nanshe.imp.segment.ExtendedRegionProps method) get_matching_grouped_paths() (in module nanshe.io.hdf5.search) get_matching_grouped_paths_found() (in module nanshe.io.hdf5.search) get_matching_paths() (in module nanshe.io.hdf5.search) get_matching_paths_groups() (in module nanshe.io.hdf5.search) get_multipage_tiff_shape_dtype() (in module nanshe.io.xtiff) get_multipage_tiff_shape_dtype_transformed() (in module nanshe.io.xtiff) get_neuron_dtype() (in module nanshe.imp.segment) get_one_neuron() (in module nanshe.imp.segment) get_quantiles() (in module nanshe.util.xnumpy) get_standard_tiff_array() (in module nanshe.io.xtiff) get_standard_tiff_data() (in module nanshe.io.xtiff) getSpecialLogger() (in module nanshe.util.prof) getTraceLogger() (in module nanshe.util.prof) getTraceMetaLogger() (in module nanshe.util.prof) group (nanshe.io.hdf5.serializers.HDF5MaskedDataset attribute)

H

hdf5_wrapper() (in module nanshe.io.hdf5.serializers) HDF5ArrayRecorder (class in nanshe.io.hdf5.record)

HDF5EnumeratedArrayRecorder (class in nanshe.io.hdf5.record) HDF5MaskedDataset (class in nanshe.io.hdf5.serializers)

I

index_array_to_bool_array() (in module nanshe.util.xnumpy) index_axis_at_pos() (in module nanshe.util.xnumpy)

index_enumerator() (in module nanshe.util.iters) iter_with_skip_indices() (in module nanshe.util.iters) iter_with_skip_values() (in module nanshe.util.iters)

L

lagged_generators() (in module nanshe.util.iters) lagged_generators_zipped() (in module nanshe.util.iters) line_filter() (in module nanshe.util.xnumpy)

list_indices_to_index_array() (in module nanshe.util.iters) list_indices_to_numpy_bool_array() (in module nanshe.util.iters) log_call() (in module nanshe.util.prof) log_class() (in module nanshe.util.prof)

M

main() (in module nanshe.converter) (in module nanshe.learner) (in module nanshe.registerer) MappingDiscreteGeometricDistributionGenerator (class in nanshe.misc.random_dictionary_learning_data) MappingDiscreteUniformDistributionGenerator (class in nanshe.misc.random_dictionary_learning_data) mask (nanshe.io.hdf5.serializers.HDF5MaskedDataset attribute) masks_intersection() (in module nanshe.util.xnumpy) masks_overlap_normalized() (in module nanshe.util.xnumpy)

masks_union() (in module nanshe.util.xnumpy) match_regions_properties() (in module nanshe.imp.segment) matrix_reduced_op() (in module nanshe.util.xnumpy) max_abs() (in module nanshe.util.xnumpy) memory_profiler() (in module nanshe.util.prof) merge_neuron_sets() (in module nanshe.imp.segment) merge_neuron_sets_once() (in module nanshe.imp.segment) merge_neuron_sets_repeatedly() (in module nanshe.imp.segment) min_abs() (in module nanshe.util.xnumpy)

N

name (nanshe.io.hdf5.serializers.HDF5MaskedDataset attribute) nanmax_abs() (in module nanshe.util.xnumpy) nanmin_abs() (in module nanshe.util.xnumpy) nanshe (module) nanshe.box (module) nanshe.box.spams_sandbox (module) nanshe.converter (module) nanshe.imp (module) nanshe.imp.filters (module) nanshe.imp.filters.masks (module) nanshe.imp.filters.noise (module) nanshe.imp.filters.wavelet (module) nanshe.imp.registration (module) nanshe.imp.renorm (module) nanshe.imp.segment (module) nanshe.io (module) nanshe.io.hdf5 (module) nanshe.io.hdf5.record (module) nanshe.io.hdf5.search (module) nanshe.io.hdf5.serializers (module) nanshe.io.xjson (module)

nanshe.io.xtiff (module) nanshe.learner (module) nanshe.misc (module) nanshe.misc.random_dictionary_learning_data (module) nanshe.registerer (module) nanshe.syn (module) nanshe.syn.data (module) nanshe.util (module) nanshe.util.iters (module) nanshe.util.prof (module) nanshe.util.wrappers (module) nanshe.util.xglob (module) nanshe.util.xnumpy (module) ndim (nanshe.io.hdf5.serializers.HDF5MaskedDataset attribute) noise_mask() (in module nanshe.imp.filters.noise) norm() (in module nanshe.util.xnumpy) normalize_data() (in module nanshe.imp.segment) NotNumPyStructuredArrayType numpy_structured_array_dtype_generator() (in module nanshe.util.xnumpy) numpy_structured_array_dtype_list() (in module nanshe.util.xnumpy) NumpyRandomArrayDiscreteUniformDistributionGenerator (class in nanshe.misc.random_dictionary_learning_data)

P

pair_dot_product() (in module nanshe.util.xnumpy) pair_dot_product_normalized() (in module nanshe.util.xnumpy)

pair_dot_product_partially_normalized() (in module nanshe.util.xnumpy) postprocess_data() (in module nanshe.imp.segment) preprocess_data() (in module nanshe.imp.segment)

Q

quantile() (in module nanshe.util.xnumpy)

R

read_numpy_structured_array_from_HDF5() (in module nanshe.io.hdf5.serializers) read_parameters() (in module nanshe.io.xjson) recorders (nanshe.imp.segment.ExtendedRegionProps attribute) region_properties() (in module nanshe.imp.segment) region_properties_scikit_image() (in module nanshe.imp.segment) region_properties_vigra() (in module nanshe.imp.segment) register_mean_offsets() (in module nanshe.imp.registration) remove_low_intensity_local_maxima() (in module nanshe.imp.segment) remove_prop_indices() (nanshe.imp.segment.ExtendedRegionProps method) remove_prop_mask() (nanshe.imp.segment.ExtendedRegionProps method)

remove_too_close_local_maxima() (in module nanshe.imp.segment) remove_zeroed_lines() (in module nanshe.imp.segment) renormalized_images() (in module nanshe.imp.renorm) renumber_label_image() (in module nanshe.util.xnumpy) renumber_labels() (nanshe.imp.segment.ExtendedRegionProps method) resize() (nanshe.io.hdf5.serializers.HDF5MaskedDataset method) reverse_each_element() (in module nanshe.util.iters) roll() (in module nanshe.util.xnumpy) run_multiprocessing_array_spams_trainDL() (in module nanshe.box.spams_sandbox) run_multiprocessing_queue_spams_trainDL() (in module nanshe.box.spams_sandbox)

S

shape (nanshe.io.hdf5.serializers.HDF5MaskedDataset attribute) significant_mask() (in module nanshe.imp.filters.noise) size (nanshe.io.hdf5.serializers.HDF5MaskedDataset attribute) SPAMSException split_hdf5_path() (in module nanshe.io.hdf5.serializers)

splitting_xrange() (in module nanshe.util.iters) squish() (in module nanshe.util.xnumpy) static_array_debug_recorder() (in module nanshe.io.hdf5.record) static_subgrouping_array_recorders() (in module nanshe.io.hdf5.record) symmetric_line_filter() (in module nanshe.util.xnumpy)

T

tagging_reorder_array() (in module nanshe.util.xnumpy) threshold_array() (in module nanshe.util.xnumpy) threshold_metric() (in module nanshe.util.xnumpy)

transform() (in module nanshe.imp.filters.wavelet) translate_fourier() (in module nanshe.imp.registration) truncate_masked_frames() (in module nanshe.util.xnumpy)

U

unique_mapping() (in module nanshe.util.xnumpy)

unsquish() (in module nanshe.util.xnumpy)

W

wavelet_denoising() (in module nanshe.imp.segment)

wavelet_thresholding() (in module nanshe.imp.segment)

X

xrange_with_skip() (in module nanshe.util.iters)

Z

zeroed_mean_images() (in module nanshe.imp.renorm)