magmap.cv package

Submodules

• magmap.cv.chunking module
  • SharedArr
  • SharedArrsContainer
    • SharedArrsContainer.build_pool_init()
    • SharedArrsContainer.convert_shared_arr()
    • SharedArrsContainer.setup_shared_arrs()
    • SharedArrsContainer.shared_arrs
  • get_mp_pool()
  • get_split_stack_total_shape()
  • init_shared_container()
  • is_fork()
  • merge_blobs()
  • merge_split_stack()
  • merge_split_stack2()
  • set_mp_start_method()
  • stack_splitter()
• magmap.cv.classifier module
  • ClassifyImage
    • ClassifyImage.blobs
    • ClassifyImage.classify_chunk()
    • ClassifyImage.classify_whole_image()
    • ClassifyImage.image5d
  • classify_blobs()
  • classify_patches()
  • extract_patches()
  • setup_classification_roi()
• magmap.cv.colocalizer module
  • BlobMatch
    • BlobMatch.Cols
      • BlobMatch.Cols.BLOB1
      • BlobMatch.Cols.BLOB1_ID
      • BlobMatch.Cols.BLOB2
      • BlobMatch.Cols.BLOB2_ID
      • BlobMatch.Cols.DIST
      • BlobMatch.Cols.MATCH_ID
      • BlobMatch.Cols.ROI_ID
    • BlobMatch.__repr__()
    • BlobMatch.get_blobs()
    • BlobMatch.get_blobs_all()
    • BlobMatch.get_mean_coords()
    • BlobMatch.update_blobs()
  • StackColocalizer
    • StackColocalizer.blobs
    • StackColocalizer.channels
    • StackColocalizer.colocalize_block()
    • StackColocalizer.colocalize_stack()
    • StackColocalizer.match_tol
  • colocalize_blobs()
  • colocalize_blobs_match()
  • insert_matches()
  • select_matches()
• 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
  • Blobs
    • Blobs.BLOBS_NP_VER
    • Blobs.Cols
      • Blobs.Cols.ABS_X
      • Blobs.Cols.ABS_Y
      • Blobs.Cols.ABS_Z
      • Blobs.Cols.CHANNEL
      • Blobs.Cols.CONFIRMED
      • Blobs.Cols.RADIUS
      • Blobs.Cols.REGION
      • Blobs.Cols.TRUTH
      • Blobs.Cols.X
      • Blobs.Cols.Y
      • Blobs.Cols.Z
    • Blobs.Keys
      • Blobs.Keys.BASENAME
      • Blobs.Keys.BLOBS
      • Blobs.Keys.COLOCS
      • Blobs.Keys.COLS
      • Blobs.Keys.RESOLUTIONS
      • Blobs.Keys.ROI_OFFSET
      • Blobs.Keys.ROI_SIZE
      • Blobs.Keys.VER
    • Blobs.blob_for_db()
    • Blobs.blobs
    • Blobs.blobs_in_channel()
    • Blobs.cols
    • Blobs.format_blobs()
    • Blobs.get_blob_abs_coords()
    • Blobs.get_blob_col()
    • Blobs.get_blob_confirmed()
    • Blobs.get_blob_truth()
    • Blobs.get_blobs_channel()
    • Blobs.load_blobs()
    • Blobs.multiply_blob_abs_coords()
    • Blobs.multiply_blob_rel_coords()
    • Blobs.remove_abs_blob_coords()
    • Blobs.replace_rel_with_abs_blob_coords()
    • Blobs.save_archive()
    • Blobs.set_blob_abs_coords()
    • Blobs.set_blob_channel()
    • Blobs.set_blob_col()
    • Blobs.set_blob_confirmed()
    • Blobs.set_blob_truth()
    • Blobs.shift_blob_abs_coords()
    • Blobs.shift_blob_rel_coords()
    • Blobs.shift_blobs()
    • Blobs.show_blobs_per_channel()
  • calc_overlap()
  • calc_scaling_factor()
  • detect_blobs()
  • get_blobs_in_roi()
  • get_blobs_interior()
  • meas_pruning_ratio()
  • remove_close_blobs()
  • remove_close_blobs_within_array()
  • remove_close_blobs_within_sorted_array()
  • remove_duplicate_blobs()
  • show_blob_surroundings()
  • sort_blobs()
• magmap.cv.segmenter module
  • LabelToMarkerErosion
    • LabelToMarkerErosion.erode_label()
    • LabelToMarkerErosion.labels_img
    • LabelToMarkerErosion.meas_wt()
    • LabelToMarkerErosion.set_labels_img()
    • LabelToMarkerErosion.wt_dists
  • SubSegmenter
    • SubSegmenter.atlas_edge
    • SubSegmenter.labels_img_np
    • SubSegmenter.set_images()
    • SubSegmenter.sub_segment()
  • labels_to_markers_blob()
  • labels_to_markers_erosion()
  • mask_atlas()
  • segment_from_labels()
  • segment_rw()
  • segment_ws()
  • sub_segment_labels()
  • watershed_distance()
• magmap.cv.stack_detect module
  • Blocks
    • Blocks.denoise_max_shape
    • Blocks.exclude_border
    • Blocks.max_pixels
    • Blocks.overlap
    • Blocks.overlap_base
    • Blocks.overlap_padding
    • Blocks.sub_roi_slices
    • Blocks.sub_rois_offsets
    • Blocks.tol
  • StackDetector
    • StackDetector.channel
    • StackDetector.coloc
    • StackDetector.denoise_max_shape
    • StackDetector.detect_blobs_sub_rois()
    • StackDetector.detect_sub_roi()
    • StackDetector.detect_sub_roi_from_data()
    • StackDetector.exclude_border
    • StackDetector.img
    • StackDetector.last_coord
  • StackPruner
    • StackPruner.blobs_to_prune
    • StackPruner.prune_blobs_mp()
    • StackPruner.prune_overlap()
    • StackPruner.prune_overlap_by_index()
  • StackTimes
    • StackTimes.DETECTION
    • StackTimes.PRUNING
    • StackTimes.TOTAL
  • detect_blobs_blocks()
  • detect_blobs_stack()
  • setup_blocks()
• magmap.cv.verifier module
  • find_closest_blobs_cdist()
  • match_blobs_roi()
  • meas_detection_accuracy()
  • setup_match_blobs_roi()
  • verify_rois()
  • verify_stack()