API Reference

Core

• playnano package
  • Subpackages
  • Submodules
  • playnano.afm_stack module
  • playnano.errors module
  • Module contents

Analysis

• playnano.analysis package
  • Subpackages
  • Submodules
  • playnano.analysis.base module
  • playnano.analysis.export module
  • playnano.analysis.pipeline module
  • Module contents
• playnano.analysis.base module
  • AnalysisModule
• playnano.analysis.export module
  • export_analysis_to_json()
• playnano.analysis.pipeline module
  • AnalysisPipeline
  • AnalysisRecord
• playnano.analysis.utils package
  • Submodules
  • playnano.analysis.utils.common module
  • playnano.analysis.utils.frames module
  • playnano.analysis.utils.loader module
  • playnano.analysis.utils.particles module
  • Module contents
• playnano.analysis.utils.common module
  • NumpyEncoder
  • export_to_hdf5()
  • load_analysis_from_hdf5()
  • make_json_safe()
  • safe_json_dumps()
  • sanitize_analysis_for_logging()
• playnano.analysis.utils.frames module
  • frame_summary_to_dataframe()
  • plot_frame_histogram()
• playnano.analysis.utils.loader module
  • load_analysis_module()
• playnano.analysis.utils.particles module
  • export_particle_csv()
  • flatten_particle_features()
  • plot_particle_labels_3d()

Analysis Modules

• playnano.analysis.modules package
  • Submodules
  • playnano.analysis.modules.count_nonzero module
  • playnano.analysis.modules.dbscan_clustering module
  • playnano.analysis.modules.feature_detection module
  • playnano.analysis.modules.k_means_clustering module
  • playnano.analysis.modules.log_blob_detection module
  • playnano.analysis.modules.particle_tracking module
  • playnano.analysis.modules.x_means_clustering module
  • Module contents
• playnano.analysis.modules.count_nonzero module
  • CountNonzeroModule
• playnano.analysis.modules.dbscan_clustering module
  • DBSCANClusteringModule
• playnano.analysis.modules.feature_detection module
  • FeatureDetectionModule
• playnano.analysis.modules.k_means_clustering module
  • KMeansClusteringModule
• playnano.analysis.modules.log_blob_detection module
  • LoGBlobDetectionModule
• playnano.analysis.modules.particle_tracking module
  • ParticleTrackingModule
• playnano.analysis.modules.x_means_clustering module
  • XMeansClusteringModule
  • compute_bic()
  • core_xmeans()
  • initialize_centers()

Processing

• playnano.processing package
  • Submodules
  • playnano.processing.core module
  • playnano.processing.filters module
  • playnano.processing.mask_generators module
  • playnano.processing.masked_filters module
  • playnano.processing.pipeline module
  • playnano.processing.stack_edit module
  • playnano.processing.video_processing module
  • Module contents
• playnano.processing.core module
  • process_stack()
• playnano.processing.filters module
  • gaussian_filter()
  • polynomial_flatten()
  • register_filters()
  • remove_plane()
  • row_median_align()
  • zero_mean()
• playnano.processing.mask_generators module
  • mask_adaptive()
  • mask_below_threshold()
  • mask_mean_offset()
  • mask_morphological()
  • mask_threshold()
  • register_masking()
• playnano.processing.masked_filters module
  • polynomial_flatten_masked()
  • register_mask_filters()
  • remove_plane_masked()
  • row_median_align_masked()
  • zero_mean_masked()
• playnano.processing.pipeline module
  • ProcessingPipeline
• playnano.processing.stack_edit module
  • Functions
  • drop_frame_range()
  • drop_frames()
  • register_stack_edit_processing()
  • select_frames()
• playnano.processing.video_processing module
  • align_frames()
  • crop_square()
  • intersection_crop()
  • register_video_processing()
  • replace_nan()
  • rolling_frame_align()
  • temporal_mean_filter()
  • temporal_median_filter()

IO

• playnano.io package
  • Subpackages
  • Submodules
  • playnano.io.data_loaders module
  • playnano.io.export_data module
  • playnano.io.gif_export module
  • playnano.io.loader module
  • Module contents
• playnano.io.data_loaders module
  • Functions
  • load_h5_bundle()
  • load_npz_bundle()
  • load_ome_tiff_stack()
• playnano.io.export_data module
  • Supported formats
  • check_path_is_path()
  • export_bundles()
  • save_h5_bundle()
  • save_npz_bundle()
  • save_ome_tiff_stack()
• playnano.io.formats package
  • Submodules
  • playnano.io.formats.read_asd module
  • playnano.io.formats.read_h5jpk module
  • playnano.io.formats.read_jpk_folder module
  • playnano.io.formats.read_spm_folder module
  • Module contents
• playnano.io.formats.read_asd module
  • load_asd_file()
• playnano.io.formats.read_h5jpk module
  • apply_z_unit_conversion()
  • load_h5jpk()
• playnano.io.formats.read_jpk_folder module
  • load_jpk_folder()
• playnano.io.formats.read_spm_folder module
  • load_spm_folder()
  • parse_spm_header()
• playnano.io.gif_export module
  • Dependencies
  • create_gif_with_scale_and_timestamp()
  • export_gif()
• playnano.io.loader module
  • get_loader_for_file()
  • get_loader_for_folder()
  • load_afm_stack()

CLI

• playnano.cli package
  • Submodules
  • playnano.cli.actions module
  • playnano.cli.entrypoint module
  • playnano.cli.handlers module
  • playnano.cli.utils module
  • Module contents
• playnano.cli.actions module
• playnano.cli.entrypoint module
• playnano.cli.handlers module
• playnano.cli.utils module
  • ask_for_analysis_params()
  • ask_for_processing_params()
  • get_processing_step_type()
  • is_valid_analysis_step()
  • is_valid_step()
  • parse_analysis_file()
  • parse_analysis_string()
  • parse_processing_file()
  • parse_processing_string()

GUI

• playnano.gui package
  • Subpackages
  • Submodules
  • playnano.gui.main module
  • playnano.gui.window module
  • Module contents
• playnano.gui.main module
• playnano.gui.widgets package
  • Submodules
  • playnano.gui.widgets.controls module
  • playnano.gui.widgets.viewer module
  • Module contents
• playnano.gui.widgets.controls module
• playnano.gui.widgets.viewer module
• playnano.gui.window module