utils

exception bigfeta.utils.BigFetaException

Bases: Exception

BigFeta exception

bigfeta.utils.blocks_from_tilespec_pair(ptspec, qtspec, match, pcol, qcol, ncol, matrix_assembly)

create sparse matrix block from tilespecs and pointmatch

Parameters:
  • ptspec (renderapi.tilespec.TileSpec) – ptspec.tforms[-1] is an AlignerTransform object
  • qtspec (renderapi.tilespec.TileSpec) – qtspec.tforms[-1] is an AlignerTransform object
  • match (dict) – pointmatch between tilepairs
  • pcol (int) – index for start of column entries for p
  • qcol (int) – index for start of column entries for q
  • ncol (int) – total number of columns in sparse matrix
  • matrix_assembly (dict) – see class matrix_assembly in schemas, sets npts
Returns:

  • pblock (scipy.sparse.csr_matrix) – block for the p tilespec/match entry. The full block can be had from pblock - qblock, but, it is a little faster to do vstack and then subtract, so p and q remain separate
  • qblock (scipy.sparse.csr_matrix) – block for the q tilespec/match entry
  • w (numpy.ndarray) – weights for the rows in pblock and qblock
bigfeta.utils.concatenate_results(results, pop_rhs=False, pop_zlist=False)

row concatenates sparse matrix blocks and associated vectors

Parameters:results (list) – dict with keys “block”, “weights”, “rhs”, “zlist”
Returns:
bigfeta.utils.create_or_set_loading(stack)

creates a new stack or sets existing stack to state LOADING

Parameters:stack (bigfeta.schemas.output_stack) –
bigfeta.utils.determine_zvalue_pairs(resolved, depths)

creates a lidt of pairs by z that will be included in the solve

Parameters:
Returns:

pairs – keys are z values and sectionIds for each pair
Return type:

List of dict
bigfeta.utils.get_matches(iId, jId, collection, dbconnection)

retrieve point correspondences

Parameters:
Returns:

matches – standard render/mongo representation of point matches
Return type:

List of dict
bigfeta.utils.get_resolved_from_z(stack, tform_name, fullsize, order, z)
retrieves a ResolvedTiles object from some source and mutates the
final transform for each tilespec into an AlignerTransform object
Parameters:
  • stack (bigfeta.schemas.input_stack) –
  • tform_name (str) – specifies which transform to mutate into (solve for)
  • fullsize (bool) – passed as kwarg to the bigfeta.transform.AlignerTransform
  • order (int) – passed as kwarg to the bigfeta.transform.AlignerTransform
  • z (int or float) – z value for one section
Returns:

resolved
Return type:

renderapi.resolvedtiles.ResolvedTiles
bigfeta.utils.get_resolved_tilespecs(stack, tform_name, pool_size, zvals, fullsize=False, order=2)
retrieves ResolvedTiles objects from some source and mutates the
final transform for each tilespec into an AlignerTransform object
Parameters:
  • stack (bigfeta.schemas.input_stack) –
  • tform_name (str) – specifies which transform to mutate into (solve for)
  • pool_size (int) – level of parallelization for parallel reads
  • fullsize (bool) – passed as kwarg to the bigfeta.transform.AlignerTransform
  • order (int) – passed as kwarg to the bigfeta.transform.AlignerTransform
  • zvals (numpy.ndarray) – z values for desired sections
Returns:

resolved
Return type:

renderapi.resolvedtiles.ResolvedTiles
bigfeta.utils.get_stderr_stdout(outarg)

helper function for suppressing render output

Parameters:outarg (str) – from input schema “render_output”
Returns:stdeo – destination for stderr and stdout
Return type:file handle or None
bigfeta.utils.get_z_values_for_stack(stack, zvals)
multi-interface wrapper to find overlapping z values
between a stack and the requested range.
Parameters:
  • stack (bigfeta.schema.input_stack) –
  • zvals (numpy.ndarray) – int or float. input z values
Returns:

zvals – int or float. overlapping z values
Return type:

numpy.ndarray
bigfeta.utils.make_dbconnection(collection, which='tile', interface=None)

creates a multi-interface object for stacks and collections

Parameters:
  • collection (bigfeta.schemas.db_params) –
  • which (str) – switch for having mongo retrieve reference transforms
  • interface (str or None) – specification to override bigfeta.schemas.db_params.db_interface
Returns:

dbconnection – a multi-interface object used by other functions in bigfeta.utils
Return type:

obj
bigfeta.utils.message_from_solve_results(results)
create summarizing string message about solve for
logging
Parameters:results (dict) – returned from bigfeta.utils.solve() or read from external solver results
Returns:message – human-readable summary message
Return type:str
bigfeta.utils.ready_transforms(tilespecs, tform_name, fullsize, order)

mutate last transform in each tilespec to be an AlignerTransform

Parameters:
  • tilespecs (List) – renderapi.tilespec.TileSpec objects.
  • tform_name (str) – intended destination type for the mutation
  • fullsize (bool) – passed as kwarg to AlignerTransform
  • order (int) – passed as kwarg to AlignerTransform
bigfeta.utils.set_complete(stack)

set stack state to COMPLETE

Parameters:stack (bigfeta.schemas.output_stack) –
bigfeta.utils.transform_match(match, ptspec, qtspec, apply_list, tforms)
transform the match coordinates through a subset of the
tilespec transform list
Parameters:
Returns:

match – one match object, with p and q transformed
Return type:

dict
bigfeta.utils.update_tilespecs(resolved, x)

update tilespecs with new solution

Parameters:
bigfeta.utils.write_chunk_to_file(fname, c, file_weights, rhs)

write a sub-matrix to an hdf5 file for an external solve

Parameters:
bigfeta.utils.write_reg_and_tforms(args, resolved, metadata, tforms, reg)

write regularization and transforms (x0) to hdf5

Parameters:
bigfeta.utils.write_to_new_stack(resolved, output_stack, outarg, overwrite_zlayer, args, results)

write results to render or file output

Parameters:
Returns:

output_stack – representation of bigfeta.schemas.output_stack
Return type:

dict