API for OpenSpecy
Analyze, Process, Identify, and Share Raman and (FT)IR Spectra

Global functions
.ai_prediction_table Source code
.append_match_metadata Source code
.append_particle_matches Source code
.append_specs_transformation Source code
.apply_specs_background_result Source code
.apply_spectra Source code
.artifact_ratio_metrics Source code
.artifact_ratio_metrics_block Source code
.as_specs_values Source code
.as_spectra_matrix Source code
.attach_particle_image Source code
.auto_restrict_tail Source code
.automate_particle_filespec_region Source code
.axes_to_hilbert_transpose Source code
.axis_cell_widths Source code
.background_specs Source code
.baseline_poly_fit Source code
.baseline_poly_fit_qr Source code
.baseline_poly_qr Source code
.bitmat_to_coords Source code
.bits_to_uint32 Source code
.bits_to_uint64_parts Source code
.blockwise_retained_capacity Source code
.bmp_int Source code
.bmp_uint Source code
.breakpoint_snr_matrix Source code
.candidate_rejected_regions Source code
.check_intensity_step_shape Source code
.check_specs_hilbert_invariants Source code
.check_specs_memory Source code
.check_specs_pca Source code
.chkf Source code
.clip_image_coords Source code
.clip_particle_overlay_extent Source code
.col_sd Source code
.collapse_particle_units Source code
.compact_specs_coords Source code
.compatible_hilbert_specs Source code
.compatible_specs Source code
.conform_intens Source code
.conform_intens_matrix Source code
.conform_mean_up_matrix Source code
.contiguous_true_runs Source code
.coords_to_bitmat Source code
.copy_open_specy_attributes Source code
.cor_spec_inputs Source code
.decode_specs_metadata Source code
.def_features Source code
.default_specs_n_components Source code
.dequantize_specs_hilbert Source code
.derivative Source code
.derivative_matrix Source code
.detect_mad_prominence_spikes Source code
.detect_prominence_spikes Source code
.detect_residual_spikes Source code
.detect_saturation Source code
.detect_spikes Source code
.dominant_red_frame_lines Source code
.empty_full_assessment Source code
.empty_spike_candidates Source code
.empty_spike_regions Source code
.encode_specs_metadata Source code
.envi_background_result Source code
.envi_background_result_from_mapping Source code
.envi_build_specs Source code
.envi_read_spec Source code
.envi_spatial_calibration Source code
.envi_specs_metadata Source code
.envi_wavenumbers Source code
.estimate_temperature_matrix Source code
.expand_assessment_report Source code
.expand_specs_matches Source code
.expand_standard_assessment_report Source code
.eye Source code
.fast_correlation Source code
.filespec_acquire_lock Source code
.filespec_assert_not_source Source code
.filespec_atomic_save_rds Source code
.filespec_axis Source code
.filespec_backend Source code
.filespec_bands Source code
.filespec_block_positions Source code
.filespec_bounded_chunk_size Source code
.filespec_cache_commit Source code
.filespec_cache_key Source code
.filespec_cache_path Source code
.filespec_cache_root Source code
.filespec_chunk_size_for_bytes Source code
.filespec_collapse_connected_mean Source code
.filespec_column_chunk_id Source code
.filespec_consecutive_runs Source code
.filespec_descriptor_target Source code
.filespec_envi_pair Source code
.filespec_envi_read_values Source code
.filespec_envi_targets Source code
.filespec_envi_type Source code
.filespec_fingerprint Source code
.filespec_h5_visual_descriptor Source code
.filespec_image_identity Source code
.filespec_index Source code
.filespec_match_prepared_best Source code
.filespec_materialize_visual Source code
.filespec_materialized_metadata Source code
.filespec_mean_features Source code
.filespec_member_table Source code
.filespec_n_spectra Source code
.filespec_open_envi Source code
.filespec_open_h5 Source code
.filespec_particle_chunks Source code
.filespec_particle_display Source code
.filespec_particle_matches Source code
.filespec_particle_snr Source code
.filespec_positions Source code
.filespec_positive_scalar Source code
.filespec_prepare_correlation_reference Source code
.filespec_read Source code
.filespec_read_block Source code
.filespec_read_envi Source code
.filespec_read_h5 Source code
.filespec_read_values Source code
.filespec_regions Source code
.filespec_release_lock Source code
.filespec_retained_mean_capacity Source code
.filespec_roi Source code
.filespec_scalar Source code
.filespec_smoothed_values Source code
.filespec_source_path Source code
.filespec_stop_unsupported Source code
.filespec_unique_existing Source code
.filespec_validate_members Source code
.filespec_validate_object Source code
.filespec_validate_source Source code
.filespec_values_to_OpenSpecy Source code
.filespec_write_envi Source code
.fill_peaks_correct Source code
.fill_peaks_matrix Source code
.fill_peaks_parameters Source code
.fill_peaks_smooth Source code
.filter_particle_matches Source code
.fit_specs_hilbert Source code
.fit_specs_pca_weighted Source code
.flatten_range Source code
.gaussian_kernel_half_width Source code
.h5_dataset_dims Source code
.h5_intersecting_tiles Source code
.h5_map_stage_extent Source code
.h5_meta_first Source code
.h5_metadata_number Source code
.h5_metadata_text Source code
.h5_mosaic_image_names Source code
.h5_mosaic_stage_tiles Source code
.h5_region_metadata Source code
.h5_region_stage Source code
.h5_region_stage_from_metadata Source code
.h5_scalar_value Source code
.h5_spatial_calibrations Source code
.h5_spectral_dim Source code
.h5_stage_extent Source code
.h5_stitch_region_mosaic Source code
.h5_wavenumbers Source code
.h5_xml_scalar_vars Source code
.hilbert_code_numeric Source code
.hilbert_decode_codes Source code
.hilbert_encode_coords Source code
.hilbert_transpose_to_axes Source code
.ignored_value_matrix Source code
.ignored_value_vector Source code
.image_edge_tolerance Source code
.image_rgb_array Source code
.indexed_argument Source code
.infer_visual_map_dim Source code
.intensity_na_plan Source code
.inverse_specs_pca Source code
.is_hilbert_specs Source code
.join_particle_cell_matches Source code
.join_particle_display_matches Source code
.join_particle_map_matches Source code
.kmeans_specs Source code
.lib_build_core Source code
.library_match_groups Source code
.library_revision Source code
.linear_spike_band_risk Source code
.local_residual_metrics Source code
.local_residual_metrics_complete Source code
.local_residual_metrics_matrix Source code
.logical_runs Source code
.manage_na_ignore Source code
.map_to_image_coords Source code
.match_spec_blockwise Source code
.match_specs_hilbert Source code
.matrix_adj_neg Source code
.matrix_ginv Source code
.matrix_mean_replace Source code
.merge_spike_regions Source code
.new_spatial_calibration Source code
.normalize_artifact_spectra Source code
.normalize_hilbert_code_values Source code
.normalize_hilbert_limits Source code
.normalize_image_channel Source code
.normalize_particle_outputs Source code
.normalize_particle_samples Source code
.normalize_particle_strategy Source code
.normalize_specs_steps Source code
.onAttach Source code
.open_specy_to_specs Source code
.openspecy_app_packages Source code
.openspecy_bundled_shiny_files Source code
.openspecy_find_shiny_app_path Source code
.openspecy_is_shiny_app_dir Source code
.openspecy_library_catalog Source code
.openspecy_require_shiny_packages Source code
.openspecy_shiny_app_path Source code
.openspecy_validate_bundled_shiny_app Source code
.particle_background_material Source code
.particle_cell_range Source code
.particle_collapse_function Source code
.particle_companion_image Source code
.particle_connected_regions Source code
.particle_connected_unit_geometry Source code
.particle_constant_unit_metadata Source code
.particle_details_table Source code
.particle_feret_dimensions Source code
.particle_filespec_output_names Source code
.particle_geometric_mean Source code
.particle_grid_raster Source code
.particle_integer Source code
.particle_kmeans_groups Source code
.particle_local_seed Source code
.particle_logical_mask Source code
.particle_map_area_um2 Source code
.particle_material_grid Source code
.particle_material_palette Source code
.particle_material_vector Source code
.particle_membership_rows Source code
.particle_origin Source code
.particle_partition_colors Source code
.particle_plot_data Source code
.particle_positive_integer Source code
.particle_progress Source code
.particle_reduce_unit_spectra Source code
.particle_scalar_number Source code
.particle_shared_pca Source code
.particle_source_vector Source code
.particle_strategy_map Source code
.particle_strategy_result Source code
.particle_stream_progress Source code
.particle_summary_table Source code
.particle_threshold_state Source code
.particle_threshold_state_message Source code
.particle_uncertainty_columns Source code
.partition_particle_map Source code
.pca_specs Source code
.planck_radiance_wavenumber Source code
.plot_particle_material_grid Source code
.predict_specs_pca Source code
.prepare_spike_corrections Source code
.process_for_particle_match Source code
.process_intensity_step Source code
.quadratic_spike_interpolation Source code
.quantize_specs_hilbert Source code
.read_envi_bip_background Source code
.read_envi_block Source code
.read_envi_header Source code
.read_envi_specs Source code
.read_envi_spectra Source code
.read_h5_file_metadata Source code
.read_h5_visual_image Source code
.read_particle_sample Source code
.read_visual_bmp_bytes Source code
.read_visual_bmp_file Source code
.read_visual_image Source code
.reject_removed_particle_args Source code
.relative_sd Source code
.report_match_progress Source code
.require_columns Source code
.resolve_hilbert_bits Source code
.resolve_particle_palette Source code
.resolve_visual_image Source code
.restrict_saturation Source code
.rms_color_channel Source code
.round_detection_limit Source code
.rows_without_ignored_values Source code
.run_sig_over_noise_complete_matrix Source code
.run_sig_over_noise_matrix Source code
.run_sig_over_noise_vector Source code
.same_specs_variables Source code
.saturation_axis_breaks Source code
.scale_correlation_spectra Source code
.set_spatial_calibration Source code
.sgfilt Source code
.sgfilt_matrix Source code
.sgolay_filter Source code
.sig_noise_entropy Source code
.sig_noise_simple_matrix Source code
.smooth_particle_sample Source code
.specs_attr Source code
.specs_attrs Source code
.specs_background_intensity Source code
.specs_model_metadata Source code
.specs_particle_strategy Source code
.specs_source_index Source code
.specs_value_index Source code
.specs_value_weights Source code
.specs_values_for_cor Source code
.specs_variables_for_open_specy Source code
.spectra_colnames Source code
.spectra_have_valid_values Source code
.spectra_ignore_info Source code
.spectra_ignore_info_from_mask Source code
.spectral_point_values Source code
.spike_diagnostic Source code
.spike_findpeak_intervals Source code
.spike_left_crossing Source code
.spike_local_peaks Source code
.spike_peak_feature Source code
.spike_raw_mad_diff Source code
.spike_result_signature Source code
.spike_right_crossing Source code
.split_h5_atomic_copy Source code
.split_h5_atomic_save_rds Source code
.split_h5_copy_mosaic Source code
.split_h5_file_label Source code
.split_h5_paths Source code
.split_h5_regions_native Source code
.split_line Source code
.subset_open_specy_columns Source code
.subset_specs_for_decompression Source code
.supported_spectrum_extensions Source code
.thermal_block_size Source code
.thermal_common_radiance Source code
.thermal_curvature_coefficients Source code
.thermal_digest Source code
.thermal_empty_fit Source code
.thermal_filespec_index Source code
.thermal_fit_complete Source code
.thermal_fit_range Source code
.thermal_metadata_values Source code
.thermal_openspecy_index Source code
.thermal_prepare_scores Source code
.thermal_reject_dots Source code
.thermal_result_table Source code
.thermal_score_matrix_direct Source code
.thermal_select_local_minimum Source code
.thermal_summarize_block Source code
.thermal_temperature_range Source code
.thermal_trapezoid_weights Source code
.thermal_valid_denominator Source code
.thermal_validate_axis Source code
.thermal_validate_radiance_source Source code
.thermal_validate_radiance_unit Source code
.thermal_validate_spectra Source code
.top_match_rows Source code
.transform_specs Source code
.uint32_max Source code
.uint32_to_bits Source code
.uint64_parts_to_bits Source code
.validate_grouped_top_n Source code
.validate_hilbert_bits Source code
.validate_image_corner Source code
.validate_match_batch_size Source code
.validate_particle_sn_thresholds Source code
.validate_particle_specs_steps Source code
.validate_specs_background Source code
.validate_specs_background_filter Source code
.validate_specs_coords_model Source code
.validate_specs_metadata_model Source code
.validate_specs_steps Source code
.validate_spectral_point Source code
.validate_spike_input Source code
.validate_spike_parameters Source code
.validate_spike_transaction Source code
.visual_image_raster Source code
.visual_image_region Source code
.visual_map_dim Source code
.weighted_specs_kmeans Source code
.whittaker Source code
.whittaker_matrix Source code
OpenSpecy Man page Source code
OpenSpecy-package Man page
Specs Man page Source code
`%||%` Source code
add_visual_image Man page Source code
adj_intens Man page Source code
adj_intens.OpenSpecy Man page Source code
adj_intens.default Man page Source code
adj_neg Man page Source code
adj_res Man page Source code
adj_wave Man page Source code
adj_wave.OpenSpecy Man page Source code
adj_wave.default Man page Source code
ai_classify Man page Source code
ai_classify.OpenSpecy Man page Source code
ai_classify.default Man page Source code
apmdt Source code
area_under_band Man page Source code
area_under_band.OpenSpecy Man page Source code
area_under_band.default Man page Source code
as.data.frame.OpenSpecy Man page Source code
as.data.table.OpenSpecy Man page Source code
as_OpenSpecy Man page Source code
as_OpenSpecy.OpenSpecy Man page Source code
as_OpenSpecy.Specs Man page Source code
as_OpenSpecy.data.frame Man page Source code
as_OpenSpecy.default Man page Source code
as_OpenSpecy.hyperSpec Man page Source code
as_OpenSpecy.list Man page Source code
as_Specs Man page Source code
as_Specs.FileSpecs Man page Source code
as_Specs.OpenSpecy Man page Source code
as_Specs.Specs Man page Source code
as_Specs.default Man page Source code
as_hyperSpec Man page Source code
assess_lib Man page
assess_spec Man page Source code
assess_spec.OpenSpecy Man page Source code
assess_spec.default Man page Source code
automate_particle_analysis Man page Source code
automate_particle_analysis.FileSpecs Man page Source code
automate_particle_analysis.default Man page Source code
batch_detection_limit Man page Source code
build_lib Man page Source code
build_model_lib Man page
c_spec Man page Source code
c_spec.OpenSpecy Man page Source code
c_spec.default Man page Source code
c_spec.list Man page Source code
calc_window_points Man page Source code
calc_window_points.OpenSpecy Man page Source code
calc_window_points.default Man page Source code
calculate_emissivity Man page Source code
calculate_emissivity.OpenSpecy Man page Source code
calculate_emissivity.default Man page Source code
check_OpenSpecy Man page Source code
check_Specs Man page Source code
check_Specs.FileSpecs Man page Source code
check_Specs.Specs Man page Source code
check_Specs.default Man page Source code
check_lib Man page Source code
collapse_spec Man page Source code
collapse_spec.FileSpecs Man page Source code
collapse_spec.OpenSpecy Man page Source code
collapse_spec.Specs Man page Source code
collapse_spec.default Man page Source code
conform_res Man page Source code
conform_spec Man page Source code
conform_spec.OpenSpecy Man page Source code
conform_spec.default Man page Source code
cor_spec Man page Source code
cor_spec.FileSpecs Man page Source code
cor_spec.OpenSpecy Man page Source code
cor_spec.Specs Man page Source code
cor_spec.default Man page Source code
correct_spike Man page Source code
correct_spike.OpenSpecy Man page Source code
correct_spike.default Man page Source code
crowd_lookup Man page Source code
decode_specs_hilbert Man page Source code
decompress_spec Man page Source code
decompress_spec.FileSpecs Man page Source code
decompress_spec.Specs Man page Source code
decompress_spec.default Man page Source code
dedupe_spec Man page
def_features Man page Source code
def_features.FileSpecs Man page Source code
def_features.OpenSpecy Man page Source code
def_features.Specs Man page Source code
def_features.default Man page Source code
detect_image_origin Man page Source code
encode_specs_hilbert Man page Source code
estimate_temperature Man page Source code
estimate_temperature.FileSpecs Man page Source code
estimate_temperature.OpenSpecy Man page Source code
estimate_temperature.default Man page Source code
fill_spec Man page Source code
fill_spec.OpenSpecy Man page Source code
fill_spec.default Man page Source code
filter_spec Man page Source code
filter_spec.OpenSpecy Man page Source code
filter_spec.default Man page Source code
fit_specs_pca Man page Source code
flatten_range Man page Source code
flatten_range.OpenSpecy Man page Source code
flatten_range.default Man page Source code
gen_grid Man page Source code
get_lib Man page Source code
get_metadata Man page Source code
get_metadata.OpenSpecy Man page Source code
get_metadata.default Man page Source code
head.OpenSpecy Man page Source code
heatmap_spec Man page
heatmap_spec.OpenSpecy Man page
heatmap_spec.default Man page
human_ts Man page Source code
ident_spec Man page Source code
interactive_plot Man page
interactive_plot.OpenSpecy Man page
interactive_plot.default Man page
io_spec Man page
is_OpenSpecy Man page Source code
is_Specs Man page Source code
is_empty_vector Man page Source code
join_lib_metadata Man page
join_material_hierarchy Man page
lib_clean_metadata Man page
lib_clean_name Man page
lib_metadata_name_lookup Man page
load_lib Man page Source code
make_lib_lookup_template Man page
make_rel Man page Source code
make_rel.OpenSpecy Man page Source code
make_rel.default Man page Source code
make_rel.matrix Man page Source code
manage_na Man page Source code
manage_na.OpenSpecy Man page Source code
manage_na.default Man page Source code
match_spec Man page Source code
match_spec.FileSpecs Man page Source code
match_spec.OpenSpecy Man page Source code
match_spec.Specs Man page Source code
match_spec.default Man page Source code
material_percentage_uncertainty Man page Source code
max_cor_named Man page Source code
mean_replace Man page Source code
merge_map Man page Source code
merge_map.OpenSpecy Man page Source code
merge_map.default Man page Source code
merge_map.list Man page Source code
minimum_detectable_amount Man page Source code
model_class_weights Man page Source code
open_specs Man page Source code
openspecy Man page
os_similarity Man page Source code
os_similarity.OpenSpecy Man page Source code
os_similarity.default Man page Source code
particle_image Man page Source code
peak_ratio Man page Source code
peak_ratio.OpenSpecy Man page Source code
peak_ratio.default Man page Source code
plot.OpenSpecy Man page Source code
plot.OpenSpecyParticleAnalysis Man page Source code
plotly_spec Man page Source code
plotly_spec.OpenSpecy Man page Source code
plotly_spec.default Man page Source code
point_intensity Man page Source code
point_intensity.OpenSpecy Man page Source code
point_intensity.default Man page Source code
predict_class_reference Man page
print.FileSpecs Man page Source code
print.OpenSpecy Man page Source code
process_spec Man page Source code
process_spec.OpenSpecy Man page Source code
process_spec.default Man page Source code
prune_lib Man page
raman_hdpe Man page
read_any Man page Source code
read_asp Man page Source code
read_envi Man page Source code
read_extdata Man page Source code
read_h5 Man page Source code
read_jdx Man page Source code
read_many Man page Source code
read_opus Man page Source code
read_opus_raw Man page Source code
read_spa Man page Source code
read_spc Man page Source code
read_spec Man page Source code
read_specs Man page Source code
read_text Man page Source code
read_zip Man page Source code
rebuild_lib_artifacts Man page Source code
recovery_rate Man page Source code
reduce_lib Man page
restrict_range Man page Source code
restrict_range.OpenSpecy Man page Source code
restrict_range.default Man page Source code
rm_lib Man page Source code
run_app Man page Source code
sample_spec Man page Source code
sample_spec.OpenSpecy Man page Source code
sample_spec.default Man page Source code
sig_noise Man page Source code
sig_noise.OpenSpecy Man page Source code
sig_noise.default Man page Source code
smooth_intens Man page Source code
smooth_intens.OpenSpecy Man page Source code
smooth_intens.default Man page Source code
spatial_smooth Man page Source code
spec_res Man page Source code
spec_res.OpenSpecy Man page Source code
spec_res.default Man page Source code
specs_background_filter Man page Source code
specs_background_mask Man page Source code
specs_coordinates Man page Source code
specs_metadata Man page Source code
specs_source_count Man page Source code
specs_source_values Man page Source code
split_h5 Man page Source code
split_spec Man page Source code
split_spec.FileSpecs Man page Source code
split_spec.default Man page Source code
subtr_baseline Man page Source code
subtr_baseline.OpenSpecy Man page Source code
subtr_baseline.default Man page Source code
summary.OpenSpecy Man page Source code
test_lib Man page
train_spec_model Man page
visual_image Man page Source code
write_spec Man page Source code
write_spec.FileSpecs Man page Source code
write_spec.OpenSpecy Man page Source code
write_spec.default Man page Source code
write_specs Man page Source code
write_specs.FileSpecs Man page Source code
write_specs.Specs Man page Source code
write_specs.default Man page Source code
OpenSpecy documentation built on Oct. 6, 2026, 1:07 a.m.