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opener

ngtools.opener

General-purpose byte stream opener.

Classes:

Name Description
open

General-purpose stream opener.
chain

Chain multiple file objects.

Functions:

Name Description
stringify_path

Ensure that the input is a str or a file-like object.
parse_protocols

Parse protocols out of a url.
fsopen

Open a file with fsspec (authentify if needed).
filesystem

Return the fsspec filesystem corresponding to a protocol or URI.
exists

Check that the file or directory pointed by a URI exists.
linc_auth_opt

Create fsspec authentication options to access lincbrain data.
read_json

Read local or remote JSON file.
write_json

Write local or remote JSON file.
update_json

Update local or remote JSON file.

parse_protocols 

parse_protocols(*args, **kwargs)

Bases: parsed_protocols

Parse ngtools uri.

path property 

path

Alias for url.

with_part 

with_part(**kwargs)

Replace parts.

with_layer 

with_layer(layer)

Replace layer.

with_format 

with_format(format)

Replace format.

with_stream 

with_stream(stream)

Replace stream.

with_url 

with_url(url)

Replace url.

with_path 

with_path(path)

Replace path.

chain 

chain(*files, **kwargs)

Chain multiple file objects.

read 

read(n=None, *a, **k)

Read characters ("t") or byes ("b").

readline 

readline(n=None, *a, **k)

Read lines ("t").

readinto 

readinto(buf, *a, **k)

Read bytes into an existing buffer.

write 

write(*a, **k)

Write characters ("t") or bytes ("b").

writeline 

writeline(*a, **k)

Write lines.

peek 

peek(*a, **k)

Read the first bytes without moving the cursor.

seek 

seek(*a, **k)

Move the cursor.

tell 

tell(*a, **k)

Return the cursor position.

open 

open(fileobj, mode='rb', compression=None, open=True)

General-purpose stream opener.

Handles:

  • paths (local or url)
  • opened file-objects
  • anything that fsspec handles
  • compressed streams

Open a file from a path or url or an opened file object.

Parameters:

Name Type Description Default
fileobj path or url or file - object

Input file

 required
mode str

Opening mode

 'rb'
compression (zip, bz2, gzip, lzma, xz, infer)

Compression mode. If 'infer', guess from magic number (if mode 'r') or filename (if mode 'w').

 'zip'
auth dict

Authentication options to pass to fsspec.

 required

Returns:

Type Description
fileobj

Opened file

fileobj instance-attribute 

fileobj = stringify_path(fileobj)

The input path or file-like object

fileobjs instance-attribute 

fileobjs = []

Additional file-like objects that may be created upon opening.

mode instance-attribute 

mode = mode

Opening mode.

compression instance-attribute 

compression = compression

Compression mode.

open 

open()

Open the file.

close 

close()

Close the file object.

read 

read(*a, **k)

Read characters ("t") or byes ("b").

readline 

readline(*a, **k)

Read lines ("t").

readinto 

readinto(*a, **k)

Read bytes into an existing buffer.

write 

write(*a, **k)

Write characters ("t") or bytes ("b").

writeline 

writeline(*a, **k)

Write lines.

peek 

peek(*a, **k)

Read the first bytes without moving the cursor.

seek 

seek(*a, **k)

Move the cursor.

tell 

tell(*a, **k)

Return the cursor position.

readable 

readable()

Is stream readable.

writable 

writable()

Is stream readable.

seekable 

seekable()

Is stream readable.

async_open

Bases: open

Async version of open.

open async 

open()

Open the file.

close async 

close()

Close the file object.

read async 

read(*a, **k)

Read characters ("t") or byes ("b").

readline async 

readline(*a, **k)

Read lines ("t").

readinto async 

readinto(*a, **k)

Read bytes into an existing buffer.

write async 

write(*a, **k)

Write characters ("t") or bytes ("b").

writeline async 

writeline(*a, **k)

Write lines.

peek async 

peek(*a, **k)

Read the first bytes without moving the cursor.

seek async 

seek(*a, **k)

Move the cursor.

tell async 

tell(*a, **k)

Return the cursor position.

readable 

readable()

Is stream readable.

writable 

writable()

Is stream readable.

seekable 

seekable()

Is stream readable.

stringify_path 

stringify_path(filename)

Ensure that the input is a str or a file-like object.

linc_auth_opt 

linc_auth_opt(token=None)

Create fsspec authentication options to access lincbrain data.

These options should only be used when accessing data behind neuroglancer.lincbrain.org.

Parameters:

Name Type Description Default
token str

Your LINCBRAIN_API_KEY

 None

Returns:

Name Type Description
opt dict

options to pass to fsspec's HTTPFileSystem.

dandi_auth_opt 

dandi_auth_opt(token=None, instance='dandi')

Create fsspec authentication options to access the dandi api.

These options should only be used when accessing data behind dandi://.

Parameters:

Name Type Description Default
token str

Your DANDI_API_KEY or LINCBRAIN_API_KEY

 None
instance (dandi, linc)
"dandi"

Returns:

Name Type Description
opt dict

options to pass to fsspec's HTTPFileSystem.

filesystem 

filesystem(protocol, **opt)

Return the filesystem corresponding to a protocol or URI.

exists 

exists(uri, **opt)

Check that the file or directory pointed by a URI exists.

async_exists async 

async_exists(uri, **opt)

Check that the file or directory pointed by a URI exists.

read_json 

read_json(fileobj, *args, **kwargs)

Read local or remote JSON file.

write_json 

write_json(obj, fileobj, *args, **kwargs)

Write local or remote JSON file.

update_json 

update_json(obj, fileobj, *args, **kwargs)

Read local or remote JSON file.

fsopen 

fsopen(uri, mode='rb', compression=None)

Open a file with fsspec (authentify if needed).

fsopen_async async 

fsopen_async(uri, mode='rb', compression=None)

Open a file with fsspec (authentify if needed).