magmap package#
Subpackages#
- magmap.atlas package
- magmap.brain_globe package
- magmap.cloud package
- magmap.cv package
- Submodules
- magmap.cv.chunking module
- magmap.cv.classifier module
- magmap.cv.colocalizer module
- magmap.cv.cv_nd module
affine_nd()angle_indices()borders_distance()build_heat_map()calc_compactness()calc_isotropic_factor()carve()compactness_3d()compactness_count()crop_to_labels()exterior_nd()extract_region()filter_adaptive_size()get_bbox_region()get_label_bbox()get_label_props()get_selem()get_thresholded_regionprops()in_paint()interpolate_contours()interpolate_label_between_planes()laplacian_of_gaussian_img()make_isotropic()meas_region()perimeter_nd()radial_dist()radial_dist_diff()remove_bg_from_dil_fg()rescale_resize()rotate90()rotate_nd()signed_distance_transform()surface_area_3d()zero_crossing()
- magmap.cv.detector module
- magmap.cv.segmenter module
- magmap.cv.stack_detect module
- magmap.cv.verifier module
- Submodules
- magmap.gui package
- Submodules
- magmap.gui.atlas_editor module
- magmap.gui.atlas_threads module
- magmap.gui.event_handlers module
- magmap.gui.image_viewer module
- magmap.gui.import_threads module
- magmap.gui.pixel_display module
- magmap.gui.plot_editor module
- magmap.gui.roi_editor module
- magmap.gui.verifier_editor module
- magmap.gui.vis_3d module
- magmap.gui.vis_handler module
- magmap.gui.visualizer module
- Submodules
- magmap.io package
- Submodules
- magmap.io.cli module
- magmap.io.df_io module
add_cols_df()append_cols()coefvar_df()combine_cols()cond_to_cols_df()data_frames_to_csv()df_add()df_div()df_subtract()dict_to_data_frame()exps_by_regions()filter_dfs_on_vals()func_to_paired_cols()join_dfs()main()melt_cols()merge_csvs()merge_excels()normalize_df()pivot_with_conditions()print_data_frame()replace_vals()weight_mean()weight_std()zscore_df()
- magmap.io.export_regions module
- magmap.io.export_rois module
- magmap.io.export_stack module
- magmap.io.importer module
- magmap.io.libmag module
add_missing_keys()backup_file()combine_arrs()combine_paths()compact_float()convert_bin_magnitude()convert_indices_to_int()coords_for_indexing()copy_backup()create_symlink()crop_mid_str()dtype_within_range()enum_dict_aslist()enum_names_aslist()flatten()format_bytes()format_num()get_dict_keys_from_val()get_dtype_info()get_enum()get_filename_without_ext()get_git_commit()get_if_within()get_int()get_version()insert_before_ext()is_binary()is_int()is_nan()is_number()is_seq()last_lines()log_once()make_acronym()make_out_path()match_ext()normalize()npstr_to_array()pad_seq()print_compact()printcb()printv()remove_file()replace_seq()roll_elements()scale_slice()series_as_str()show_full_arrays()splice_before()splitext()str_to_disp()swap_elements()to_seq()transpose_1d()transpose_1d_rev()truncate_decimal_digit()warn()
- magmap.io.load_env module
- magmap.io.naming module
- magmap.io.np_io module
- magmap.io.packaging module
- magmap.io.sitk_io module
- magmap.io.sqlite module
- magmap.io.subproc_io module
- magmap.io.yaml_io module
- Submodules
- magmap.plot package
- Submodules
- magmap.plot.colormaps module
- magmap.plot.plot_2d module
- magmap.plot.plot_3d module
- magmap.plot.plot_support module
ImageOverlayerImageSyncMixinadd_scale_bar()add_vspans()alpha_blend_intersection()extract_planes()fit_frame_to_image()get_aspect_ratio()get_downsample_max_sizes()get_plane_axis()hide_axes()max_plane()save_fig()scale_axes()scale_xticks()scroll_plane()set_overview_title()set_scinot()setup_fig()setup_images_for_plane()setup_vspans()show()transpose_images()
- Submodules
- magmap.settings package
- Submodules
- magmap.settings.atlas_prof module
- magmap.settings.config module
ABAKeysAPP_NAMEAtlasLabelsAtlasMetricsClassifierDataCmapsDEFAULT_SAVEFIGDFTasksDNS_REVERSEDataClassDataClassProtocolDocsURLsFORMATS_3DHemSidesICON_PATHItkSnapLabelsLoadDataLoadIOMetaKeysMetricGroupsPLANEPOS_THRESHPREFS_PATHPlot2DTypesPlotLabelsPreProcessKeysProcessTypesRegNamesRegSuffixesRegisterTypesSTR_FNSUFFIX_BLOBSSUFFIX_BLOB_CLUSTERSSUFFIX_IMAGE5DSUFFIX_METASUFFIX_SUBIMGSmoothingMetricsSmoothingModesThemesTransformsTruthDBTruthDBModesURI_SCHEMEVerbosityapp_dirblobschannelclassifiercmap_labelsfilenamesformat_import_err()get_roi_profile()grid_search_profileimage5d_ioimg5dlabels_imglabels_img_origlabels_img_sitklabels_levellabels_metadatalabels_reflabels_scalingload_labelslog_pathloggermagnificationmatplotlib_stylemeta_dictmetadata_pathsmetadatasplot_labelsprefixprefix_outprefixesprefixes_outprefsproc_typerc_paramsreg_suffixesrgbsavefigseriesseries_listshowsuffixtruth_db_modeunit_factoruser_app_dirsverboseverbosityzoom
- magmap.settings.grid_search_prof module
- magmap.settings.logs module
- magmap.settings.prefs_prof module
- magmap.settings.profiles module
- magmap.settings.roi_prof module
- Submodules
- magmap.stats package
- magmap.tests package