zetastitcher.align.filematrix module¶

Parse input file names, compute tile coordinates.

class zetastitcher.align.filematrix.FileMatrix(input_path=None, ascending_tiles_x=True, ascending_tiles_y=True, recursive=False, equal_shape=False)¶

Bases: object

Data structures for a matrix of input files.

Attributes

Nx
Ny
full_height
full_thickness
full_width
tiles_along_X: Groups of tiles to be stitched along X.
tiles_along_Y: Groups of tiles to be stitched along Y.
tiles_along_dir: Groups of tiles to be stitched along a given direction.

Methods

`load_dir`([dir, recursive])	Look for files in `dir` recursively and populate data structures.
`slices`()	A slice is a group of tiles that share at least a `z` frame.

clear_absolute_positions
compute_end_pos
compute_nominal_positions
get_json
load_yaml
parse_and_append
process_data_frame
save_to_yaml

property Nx¶

property Ny¶

clear_absolute_positions()¶

compute_end_pos()¶

compute_nominal_positions(px_size_z, px_size_xy)¶

data_frame¶: A pandas.DataFrame object. Contains the following columns: X, Y, Z, Z_end, xsize, ysize, nfrms, filename.

property full_height¶

property full_thickness¶

property full_width¶

get_json()¶

load_dir(dir=None, recursive=False)¶

Look for files in dir recursively and populate data structures.

Parameters

dirpath

load_yaml(fname)¶

parse_and_append(name, flist, shape=None)¶

process_data_frame()¶

save_to_yaml(filename, mode)¶

slices()¶

A slice is a group of tiles that share at least a z frame.

Returns

compgenerator: A generator of graphs, one for each connected component of G, where G is the graph of tiles connected by at least a z frame.

property tiles_along_X¶

Groups of tiles to be stitched along X.

Equivalent to tiles_along_dir having sent the following tuple: (['Z', 'X', 'Y'], 'Y')

Yields

pandas.DataFrame: A group of tiles

property tiles_along_Y¶

Groups of tiles to be stitched along Y.

Equivalent to tiles_along_dir having sent the following tuple: (['Z', 'Y', 'X'], 'X')

Yields

pandas.DataFrame: A group of tiles

property tiles_along_dir¶

Groups of tiles to be stitched along a given direction.

You need to send to this generator a tuple containing:

a list for sorting the pandas.DataFrame, such as ['Z', 'Y', 'X']
an axis for grouping, such as 'Y'

Yields

pandas.DataFrame: A group of tiles

zetastitcher.align.filematrix.parse_file_name(file_name)¶

Parse fields (stage coordinates) contained in file_name.

Parameters

file_namestr: The string to be parsed

Returns

x, y, zint: The parsed stage coordinates.