jakirkham / zwatershed

Cython functions for fast watersheds and segmentation metrics

convolutional network metric scripts

• Code for fast watersheds. Code is based around code from https://bitbucket.org/poozh/watershed described in http://arxiv.org/abs/1505.00249. For use in https://github.com/naibaf7/PyGreentea.

building

conda

• conda install -c conda-forge zwatershed

pip

• pip install zwatershed

from source

• clone the repository
• run ./make.sh

requirements

• numpy, h5py, cython
• if using parallel watershed, also requires multiprocessing or pyspark
• in order to build the cython, requires a c++ compiler and boost

function api

• (segs, rand) = zwatershed_and_metrics(segTrue, aff_graph, eval_thresh_list, seg_save_thresh_list)
  • returns segmentations and metrics
  • segs: list of segmentations
    • len(segs) == len(seg_save_thresh_list)
  • rand: dict
    • rand['V_Rand']: V_Rand score (scalar)
    • rand['V_Rand_split']: list of score values
      • len(rand['V_Rand_split']) == len(eval_thresh_list)
    • rand['V_Rand_merge']: list of score values,
      • len(rand['V_Rand_merge']) == len(eval_thresh_list)
• segs = zwatershed(aff_graph, seg_save_thresh_list) - returns segmentations
  • segs: list of segmentations
    • len(segs) == len(seg_save_thresh_list)

These methods have versions which save the segmentations to hdf5 files instead of returning them

• rand = zwatershed_and_metrics_h5(segTrue, aff_graph, eval_thresh_list, seg_save_thresh_list, seg_save_path)
• zwatershed_h5(aff_graph, eval_thresh_list, seg_save_path)

All 4 methods have versions which take an edgelist representation of the affinity graph

• (segs, rand) = zwatershed_and_metrics_arb(segTrue, node1, node2, edgeWeight, eval_thresh_list, seg_save_thresh_list)
• segs = zwatershed_arb(seg_shape, node1, node2, edgeWeight, seg_save_thresh_list)
• rand = zwatershed_and_metrics_h5_arb(segTrue, node1, node2, edgeWeight, eval_thresh_list, seg_save_thresh_list, seg_save_path)
• zwatershed_h5_arb(seg_shape, node1, node2, edgeWeight, eval_thresh_list, seg_save_path)

parallel watershed - 4 steps

• a full example is given in par_ex.ipynb

1. Partition the subvolumes
   • partition_data = partition_subvols(pred_file,out_folder,max_len)
     • evenly divides the data in pred_file with the constraint that no dimension of any subvolume is longer than max_len
2. Zwatershed the subvolumes
   1. eval_with_spark(partition_data[0])
      • with spark
   2. eval_with_par_map(partition_data[0],NUM_WORKERS)
      • with python multiprocessing map
   • after evaluating, subvolumes will be saved into the out_folder directory named based on their smallest indices in each dimension (ex. path/to/out_folder/0_0_0_vol)
3. Stitch the subvolumes together
   • stitch_and_save(partition_data,outname)
     • stitch together the subvolumes in partition_data
     • save to the hdf5 file outname
       • outname['starts'] = list of min_indices of each subvolume
       • outname['ends'] = list of max_indices of each subvolume
       • outname['seg'] = full stitched segmentation
       • outname['seg_sizes'] = array of size of each segmentation
       • outname['rg_i'] = region graph for ith subvolume
4. Threshold individual subvolumes by merging
   • seg_merged = merge_by_thresh(seg,seg_sizes,rg,thresh)
     • load in these areguments from outname