Index

A

add_best_guesses_to_stats() (in module pyopia.statistics) add_cf_attributes() (in module pyopia.io)

add_depth_to_stats() (in module pyopia.statistics) apply_circular_mask() (in module pyopia.instrument.common)

B

bgstack (pyopia.pipeline.Data attribute) bright_norm() (in module pyopia.statistics)

build_initial_background_files() (pyopia.pipeline.FilesToProcess method) build_repr() (in module pyopia.pipeline) build_steps() (in module pyopia.pipeline)

C

CalculateImageStats (class in pyopia.process) CalculateStats (class in pyopia.process) check_convergence() (pyopia.simulator.silcam.SilcamSimulator method) chunk_files() (pyopia.pipeline.FilesToProcess method) CircularImageMask (class in pyopia.instrument.common) cl (pyopia.pipeline.Data attribute) classify_plot_class_rois() (in module pyopia.plotting) classify_rois() (in module pyopia.plotting) clean_bw() (in module pyopia.process) clean_stack() (in module pyopia.instrument.holo)

combine_stats_netcdf_files() (in module pyopia.io) concat_stats_netcdf_files() (in module pyopia.io) concentration_check() (in module pyopia.process) convert_raw_images() (in module pyopia.cli) correct_im_accurate() (in module pyopia.background) correct_im_fast() (in module pyopia.background) CorrectBackgroundAccurate (class in pyopia.background) CorrectBackgroundNone (class in pyopia.background) count_images_in_stats() (in module pyopia.statistics) create_kernel() (in module pyopia.instrument.holo) crop_stats() (in module pyopia.statistics)

D

d50_from_stats() (in module pyopia.statistics) d50_from_vd() (in module pyopia.statistics)

Data (class in pyopia.pipeline) docs() (in module pyopia.cli)

E

expand_bbox() (in module pyopia.process) explode_contrast() (in module pyopia.statistics) export_to_ecotaxa() (in module pyopia.cli) extract_and_scale_example_image() (in module pyopia.simulator.silcam) extract_latest_stats() (in module pyopia.statistics)

extract_nth_largest() (in module pyopia.statistics) extract_nth_longest() (in module pyopia.statistics) extract_oil() (in module pyopia.statistics) extract_particles() (in module pyopia.process) extract_roi() (in module pyopia.process)

F

filename (pyopia.pipeline.Data attribute) FilesToProcess (class in pyopia.pipeline) find_focus_imax() (in module pyopia.instrument.holo)

find_focus_sobel() (in module pyopia.instrument.holo) Focus (class in pyopia.instrument.holo) forward_transform() (in module pyopia.instrument.holo) from_filelist_file() (pyopia.pipeline.FilesToProcess method)

G

gen_roifiles() (in module pyopia.statistics) generate_config() (in module pyopia.cli) (in module pyopia.instrument.holo) (in module pyopia.instrument.silcam) (in module pyopia.instrument.uvp) get_classifier_database_from_pysilcam_blob() (in module pyopia.exampledata) get_custom_progress_bar() (in module pyopia.cli) get_example_hologram_and_background() (in module pyopia.exampledata)

get_example_model() (in module pyopia.exampledata) get_example_silc_image() (in module pyopia.exampledata) get_file_from_pysilcam_blob() (in module pyopia.exampledata) get_folder_from_holo_repository() (in module pyopia.exampledata) get_j() (in module pyopia.statistics) get_sample_volume() (in module pyopia.statistics) get_size_bins() (in module pyopia.statistics) get_spine_length() (in module pyopia.process)

I

im_corrected (pyopia.pipeline.Data attribute) im_focussed (pyopia.pipeline.Data attribute) im_masked (pyopia.pipeline.Data attribute) im_minimum (pyopia.pipeline.Data attribute) im_stack (pyopia.pipeline.Data attribute) image2blackwhite_accurate() (in module pyopia.process) image2blackwhite_fast() (in module pyopia.process) ImagePrep (class in pyopia.instrument.silcam) imbg (pyopia.pipeline.Data attribute)

imbw (pyopia.pipeline.Data attribute) imc (pyopia.pipeline.Data attribute) img (pyopia.pipeline.Data attribute) imraw (pyopia.pipeline.Data attribute) imref (pyopia.pipeline.Data attribute) imss (pyopia.pipeline.Data attribute) ini_background() (in module pyopia.background) init_project() (in module pyopia.cli) Initial (class in pyopia.instrument.holo) inverse_transform() (in module pyopia.instrument.holo)

L

Load (class in pyopia.instrument.holo) load_bayer_rgb8() (in module pyopia.instrument.silcam) load_image() (in module pyopia.instrument.holo) (in module pyopia.instrument.silcam) (in module pyopia.instrument.uvp)

load_image_stats() (in module pyopia.io) load_mono8() (in module pyopia.instrument.silcam) load_rgb8() (in module pyopia.instrument.silcam) load_stats() (in module pyopia.io) load_stats_as_dataframe() (in module pyopia.io) load_toml() (in module pyopia.io)

M

make_montage() (in module pyopia.cli) (in module pyopia.statistics) make_timeseries_vd() (in module pyopia.statistics) make_xstats() (in module pyopia.io) max_map() (in module pyopia.instrument.holo) measure_particles() (in module pyopia.process) merge_and_save_mfdataset() (in module pyopia.io) merge_mfdata() (in module pyopia.cli) MergeStats (class in pyopia.instrument.holo) modify_config() (in module pyopia.cli) module pyopia pyopia.auxillarydata pyopia.background, [1] pyopia.cli, [1] pyopia.dataexport pyopia.dataexport.ecotaxa pyopia.exampledata, [1] pyopia.instrument pyopia.instrument.common, [1] pyopia.instrument.holo, [1] pyopia.instrument.silcam, [1] pyopia.instrument.uvp, [1] pyopia.io, [1] pyopia.metadata pyopia.pipeline, [1] pyopia.plotting, [1] pyopia.process, [1] pyopia.realtime pyopia.simulator pyopia.simulator.silcam, [1] pyopia.statistics, [1] pyopia.tests pyopia.tests.test_auxillarydata pyopia.tests.test_io pyopia.tests.test_notebooks pyopia.tests.test_process pyopia.tests.test_realtime

montage_plot() (in module pyopia.plotting)

N

nc_from_nd() (in module pyopia.statistics) nc_vc_from_stats() (in module pyopia.statistics)

nd_from_stats() (in module pyopia.statistics) nd_from_stats_scaled() (in module pyopia.statistics) nd_rescale() (in module pyopia.statistics)

P

PerClassConcentration (class in pyopia.statistics) Pipeline (class in pyopia.pipeline) plot_classified_rois() (in module pyopia.plotting) prepare_chunking() (pyopia.pipeline.FilesToProcess method) print_steps() (pyopia.pipeline.Pipeline method) process() (in module pyopia.cli) process_file_list() (in module pyopia.cli) process_realtime() (in module pyopia.cli) process_synthetic_image() (pyopia.simulator.silcam.SilcamSimulator method) put_roi_in_h5() (in module pyopia.process) pyopia module pyopia.auxillarydata module pyopia.background module, [1] pyopia.cli module, [1] pyopia.dataexport module pyopia.dataexport.ecotaxa module pyopia.exampledata module, [1] pyopia.instrument module pyopia.instrument.common module, [1] pyopia.instrument.holo module, [1] pyopia.instrument.silcam module, [1]

pyopia.instrument.uvp module, [1] pyopia.io module, [1] pyopia.metadata module pyopia.pipeline module, [1] pyopia.plotting module, [1] pyopia.process module, [1] pyopia.realtime module pyopia.simulator module pyopia.simulator.silcam module, [1] pyopia.statistics module, [1] pyopia.tests module pyopia.tests.test_auxillarydata module pyopia.tests.test_io module pyopia.tests.test_notebooks module pyopia.tests.test_process module pyopia.tests.test_realtime module

R

raw_files (pyopia.pipeline.Data attribute) read_lisst_holo_info() (in module pyopia.instrument.holo) Reconstruct (class in pyopia.instrument.holo) RectangularImageMask (class in pyopia.instrument.common)

rescale_image() (in module pyopia.instrument.holo) roi_from_export_name() (in module pyopia.statistics) run() (pyopia.pipeline.Pipeline method) run_step() (pyopia.pipeline.Pipeline method)

S

Segment (class in pyopia.process) segment() (in module pyopia.process) setup_logging() (in module pyopia.cli) setup_xstats_encoding() (in module pyopia.io) shift_and_correct() (in module pyopia.background) shift_bgstack_accurate() (in module pyopia.background) shift_bgstack_fast() (in module pyopia.background) show_h5_meta() (in module pyopia.io) (in module pyopia.statistics) show_image() (in module pyopia.plotting) SilCamLoad (class in pyopia.instrument.silcam)

SilcamSimulator (class in pyopia.simulator.silcam) statextract() (in module pyopia.process) stats (pyopia.pipeline.Data attribute) statscsv_to_statshdf() (in module pyopia.statistics) StatsH5() (in module pyopia.io) StatsToDisc (class in pyopia.io) std_map() (in module pyopia.instrument.holo) step_callobj() (pyopia.pipeline.Pipeline method) steps_from_xstats() (in module pyopia.io) steps_string (pyopia.pipeline.Data attribute) steps_to_string() (in module pyopia.pipeline) synthesize() (pyopia.simulator.silcam.SilcamSimulator method)

T

timestamp (pyopia.pipeline.Data attribute) timestamp_from_filename() (in module pyopia.instrument.silcam) (in module pyopia.instrument.uvp)

to_filelist_file() (pyopia.pipeline.FilesToProcess method) trim_stats() (in module pyopia.statistics)

U

UVPLoad (class in pyopia.instrument.uvp)

V

vd_from_nd() (in module pyopia.statistics) vd_from_stats() (in module pyopia.statistics)

vd_to_nc() (in module pyopia.statistics) vd_to_nd() (in module pyopia.statistics)

W

weibull_distribution() (pyopia.simulator.silcam.SilcamSimulator method)

write_stats() (in module pyopia.io)