Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Update docs wording & example #122

Merged
merged 4 commits into from
Aug 27, 2022
Merged

Update docs wording & example #122

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
f8c3ee1
Remove named argument in example
addisonElliott Aug 27, 2022
978ab2d
nit: Fix mistake in user-guide
addisonElliott Aug 27, 2022
166cd5d
Tweaking wording for detailing writing NRRD files
addisonElliott Aug 27, 2022
beeefc2
fix
addisonElliott Aug 27, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
20 changes: 10 additions & 10 deletions docs/source/examples.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,10 @@ Basic Example

import numpy as np
import nrrd

data = np.linspace(1, 50, 50)
nrrd.write('output.nrrd', data)

data2, header = nrrd.read('output.nrrd')
print(np.all(data == data2))
>>> True
Expand All @@ -26,10 +26,10 @@ Example only reading header

import numpy as np
import nrrd

data = np.linspace(1, 50, 50)
nrrd.write('output.nrrd', data)

header = nrrd.read_header('output.nrrd')
print(header)
>>> OrderedDict([('type', 'double'), ('dimension', 1), ('sizes', array([50])), ('endian', 'little'), ('encoding', 'gzip')])
Expand All @@ -54,7 +54,7 @@ Example write and read from memory
print(header)
>>> OrderedDict([('type', 'double'), ('dimension', 1), ('sizes', array([50])), ('endian', 'little'), ('encoding', 'gzip')])

data2 = nrrd.read_data(header=header, fh=memory_nrrd)
data2 = nrrd.read_data(header, memory_nrrd)

print(np.all(data == data2))
>>> True
Expand All @@ -69,19 +69,19 @@ Example with fields and custom fields
data = np.linspace(1, 60, 60).reshape((3, 10, 2))
header = {'kinds': ['domain', 'domain', 'domain'], 'units': ['mm', 'mm', 'mm'], 'spacings': [1.0458, 1.0458, 2.5], 'space': 'right-anterior-superior', 'space directions': np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]]), 'encoding': 'ASCII', 'custom_field_here1': 24.34, 'custom_field_here2': np.array([1, 2, 3, 4])}
custom_field_map = {'custom_field_here1': 'double', 'custom_field_here2': 'int list'}

nrrd.write('output.nrrd', data, header, custom_field_map=custom_field_map)

data2, header2 = nrrd.read('output.nrrd', custom_field_map)

print(np.all(data == data2))
>>> True

print(header)
>>> {'units': ['mm', 'mm', 'mm'], 'spacings': [1.0458, 1.0458, 2.5], 'custom_field_here1': 24.34, 'space': 'right-anterior-superior', 'space directions': array([[1, 0, 0],
[0, 1, 0],
[0, 0, 1]]), 'type': 'double', 'encoding': 'ASCII', 'kinds': ['domain', 'domain', 'domain'], 'dimension': 3, 'custom_field_here2': array([1, 2, 3, 4]), 'sizes': [3, 10, 2]}

print(header2)
>>> OrderedDict([('type', 'double'), ('dimension', 3), ('space', 'right-anterior-superior'), ('sizes', array([ 3, 10, 2])), ('space directions', array([[1., 0., 0.],
[0., 1., 0.],
Expand Down
4 changes: 2 additions & 2 deletions docs/source/user-guide.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,7 @@ string list
:NRRD Syntax: <s> <s> ... <s>
:NRRD Example: this is space separated
:Python Datatype: :class:`list` of :class:`str`
:Python Example: ['this', 'is', 'string', 'separated']
:Python Example: ['this', 'is', 'space', 'separated']

quoted string list
~~~~~~~~~~~~~~~~~~
Expand Down Expand Up @@ -197,7 +197,7 @@ Some NRRD files, while prohibited by specification, may contain duplicated heade

Writing NRRD files
------------------
Writing to NRRD files can be done with the function :meth:`write`. The :obj:`filename` parameter to the function specifies the absolute or relative filename to write the NRRD file. If the :obj:`filename` extension is .nhdr, then the :obj:`detached_header` parameter is set to true automatically. If the :obj:`detached_header` parameter is set to :obj:`True` and the :obj:`filename` ends in .nrrd, then the header file will have the same path and base name as the :obj:`filename` but with an extension of .nhdr. In all other cases, the header and data are saved in the same file.
Writing to NRRD files can be done with the function :meth:`write`. The :obj:`filename` parameter specifies either an absolute or relative filename to write the NRRD file to. If the :obj:`filename` extension is .nhdr, then :obj:`detached_header` will be set to true automatically. If :obj:`detached_header` is :obj:`True` and :obj:`filename` extension is .nrrd, then the header file will have the same path and base name as :obj:`filename` but with an extension of .nhdr. In all other cases, the header and data are saved in the same file.

The :obj:`data` parameter is a :class:`numpy.ndarray` of data to be saved. :obj:`header` is an optional parameter of type :class:`dict` containing the field/values to be saved to the NRRD file.

Expand Down