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Update docs wording & example (#122)
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Remove named argument usage for NRRD in examples docs. For fh and header, these should not be named since they are primary (i.e. not optional) arguments.

Update wording on docs for user-guide section.
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addisonElliott authored Aug 27, 2022
1 parent ea92be4 commit 1df8eb3
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20 changes: 10 additions & 10 deletions docs/source/examples.rst
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.],
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4 changes: 2 additions & 2 deletions docs/source/user-guide.rst
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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.

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