phathom package

Subpackages

• phathom.atlas package
  • Module contents
• phathom.db package
  • Module contents
• phathom.io package
  • Submodules
  • phathom.io.conversion module
  • Module contents
• phathom.phenotype package
  • Module contents
• phathom.preprocess package
  • Module contents
• phathom.registration package
  • Submodules
  • phathom.registration.pcloud module
  • phathom.registration.registration module
  • Module contents
• phathom.segmentation package
  • Submodules
  • phathom.segmentation.graphcuts module
  • phathom.segmentation.partition module
  • phathom.segmentation.segmentation module
  • Module contents

Submodules

phathom.score module

phathom.test_helpers module

test_helpers.py

This file has routines needed by tests. They needed to be in a proper module.

phathom.test_helpers.check_range(args)

phathom.test_helpers.find_primes(start, end)

phathom.utils module

class phathom.utils.SharedMemory(shape, dtype)

A class to share memory between processes

Instantiate this class in the parent process and use in all processes.

For all but Linux, we use the mmap module to get a buffer for Numpy to access through numpy.frombuffer. But in Linux, we use /dev/shm which has no file backing it and does not need to deal with maintaining a consistent view of itself on a disk.

Typical use:

shm = SharedMemory((100, 100, 100), np.float32)

def do_something():

with shm.txn() as a:

a[…] = …

with multiprocessing.Pool() as pool:

pool.apply_async(do_something, args)

txn(**kwds)

A contextual wrapper of the shared memory

Returns:a view of the shared memory which has the shape and

dtype given at construction

phathom.utils.box_slice_idx(start, stop)

Creates an index tuple for a bounding box from start to stop using slices

Parameters:

• start (array-like) – index of box start
• stop (array-like) – index of box stop (index not included in result)

Returns:

idx – index tuple for bounding box

Return type:

tuple

phathom.utils.chunk_coordinates(shape, chunks)

Calculate the global coordaintes for each chunk’s starting position

Parameters:

• shape (tuple) – shape of the image to chunk
• chunks (tuple) – shape of each chunk

Returns:

start_coords – the starting indices of each chunk

Return type:

ndarray

phathom.utils.chunk_dims(img_shape, chunk_shape)

Calculate the number of chunks needed for a given image shape

Parameters:

• img_shape (tuple) – whole image shape
• chunk_shape (tuple) – individual chunk shape

Returns:

nb_chunks – a tuple containing the number of chunks in each dimension

Return type:

tuple

phathom.utils.extract_box(arr, start, stop)

Indexes arr from start to stop

Parameters:

• arr (array-like or SharedMemory) – input array to index
• start (array-like) – starting index of the slice
• stop (array-like) – ending index of the slice. The element at this index is not included.

Returns:

box – resulting box from arr

Return type:

ndarray

phathom.utils.files_in_dir(path)

Searches a path for all files

Parameters:path (str) – The directory path to check for files Returns:list of all files and subdirectories in the input path (excluding . and ..) Return type:list

phathom.utils.insert_box(arr, start, stop, data)

Indexes arr from start to stop and inserts data

Parameters:

• arr (array-like) – input array to index
• start (array-like) – starting index of the slice
• stop (array-like) – ending index of the slice. The element at this index is not included.
• data (array-like) – sub-array to insert into arr

Returns:

box – resulting box from arr

Return type:

ndarray

phathom.utils.load_metadata(path)

Loads a metadata.pkl file within provided path

Parameters:path (str) – path of a directory containing a ‘metadata.pkl’ file Returns:dictionary containing the stored metadata Return type:dict

phathom.utils.make_dir(path)

Makes a new directory at the provided path only if it doesn’t already exist.

Parameters:path (str) – The path of the directory to make

phathom.utils.pickle_load(path)

Un-pickles a file provided at the input path

Parameters:path (str) – path of the pickle file to read Returns:data that was stored in the input pickle file Return type:dict

phathom.utils.pickle_save(path, data)

Pickles data and saves it to provided path

Parameters:

• path (str) – path of the pickle file to create / overwrite
• data (dict) – dictionary with data to be pickled

phathom.utils.pmap_chunks(f, arr, chunks=None, nb_workers=None)

Maps a function over an array in parallel using chunks

The function f should take a reference to the array, a starting index, and the chunk size. Since each subprocess is handling it’s own indexing, any overlapping should be baked into f. Caution: arr may get copied if not using memmap. Use with SharedMemory or Zarr array to avoid copies.

Parameters:

• f (callable) – function with signature f(arr, start_coord, chunks). May need to use partial to define other args.
• arr (array-like) – an N-dimensional input array
• chunks (tuple, optional) – the shape of chunks to use. Default tries to access arr.chunks and falls back to arr.shape
• nb_workers (int, optional) – number of parallel processes to apply f with. Default, cpu_count

Returns:

result – list of results for each chunk

Return type:

list

phathom.utils.tifs_in_dir(path)

Searches input path for tif files

Parameters:path (str) – path of the directory to check for tif images Returns:

• tif_paths (list) – list of paths to tiffs in path
• tif_filenames (list) – list of tiff filenames (with the extension) in path

Module contents