russtorres / em_aligner_python

Python version of Khaled Khairy's EM_aligner, supporting distributed assembly and solve

EM_aligner_python

Level of support

We are planning on occasional updating this tool with no fixed schedule. Community involvement is encouraged through both issues and pull requests.

montage

for z in zlist:
    assemble from montage_matches(z)
    solve with scipy.sparse
ingest

python assemble_matrix.py --input_json montage_test.json

rough alignment

need to incorporate rigid transformation

small 3D

run 3D solve locally, will be RAM limited

for z in zlist:
    add to assembly from montage_matches(z), cross_matches(z,z+1),...,cross_matches(z,z+depth)
solve with scipy.sparse
ingest

python assemble_matrix.py --input_json small3D_test.json

large 3D

intended to assemble A locally into multiple files for input to a distributed solver

for z in zlist:
    add to assembly from montage_matches(z), cross_matches(z,z+1),...,cross_matches(z,z+depth)
    if assembly>big:
        write_new_file
        assembly = 0
solve elsewhere with PETSc
ingest

python not_ready_yet.py --input_json not_ready_yet.json
tar cvzf the_files
scp the_files.tar.gz user@big_machine:
user@big_machine$ tar -xvzf the_files.tar.gz
user@big_machine$ solve the_files
scp user@big_machine:the_solution ./
python ingest.py the_solution