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DOC: docstrings improved
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@dgursoy
dgursoy committed Apr 13, 2015
1 parent b3e6359 commit 33e9617
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Showing 11 changed files with 752 additions and 437 deletions.
138 changes: 69 additions & 69 deletions tomopy/io/data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -62,6 +62,8 @@
import warnings


__author__ = "Doga Gursoy"
__copyright__ = "Copyright (c) 2015, UChicago Argonne, LLC."
__docformat__ = 'restructuredtext en'
__all__ = ['as_shared_array',
'as_float32',
Expand All @@ -82,12 +84,12 @@ def as_shared_array(arr):
Parameters
----------
arr : ndarray
Input array
Input array.
Returns
-------
out : ndarray
Output array
out : ndarray (float32)
Output array.
"""
sarr = mp.Array(ctypes.c_float, arr.size)
sarr = np.frombuffer(sarr.get_obj(), dtype='float32')
Expand All @@ -98,17 +100,17 @@ def as_shared_array(arr):

def as_float32(arr):
"""
Convert a numpy array to ``float32``.
Convert a numpy array to float32.
Parameters
----------
arr : ndarray
Input array
Input array.
Returns
-------
out : ndarray
Output array
out : ndarray (float32)
Output array.
"""
if not isinstance(arr, np.float32):
arr = np.array(arr, dtype='float32')
Expand All @@ -117,23 +119,23 @@ def as_float32(arr):

def as_uint8(arr, dmin=None, dmax=None):
"""
Convert a numpy array to ``uint8``.
Convert a numpy array to uint8.
Parameters
----------
arr : ndarray
Input array
Input array.
dmin : scalar
Mininum value to adjust float-to-int conversion dynamic range
dmin : scalar (float)
Mininum value to adjust float-to-int conversion range.
dmax : scalar
Maximum value to adjust float-to-int conversion dynamic range
dmax : scalar (float)
Maximum value to adjust float-to-int conversion range.
Returns
-------
out : ndarray
Output array
out : ndarray (uint8)
Output array.
"""
if not isinstance(arr, np.int8):
arr = arr.copy()
Expand All @@ -154,23 +156,23 @@ def as_uint8(arr, dmin=None, dmax=None):

def as_uint16(arr, dmin=None, dmax=None):
"""
Convert a numpy array to ``uint16``.
Convert a numpy array to uint16.
Parameters
----------
arr : ndarray
Input array
Input array.
dmin : scalar
Mininum value to adjust float-to-int conversion dynamic range
dmin : scalar (float)
Mininum value to adjust float-to-int conversion range.
dmax : scalar
Maximum value to adjust float-to-int conversion dynamic range
dmax : scalar (float)
Maximum value to adjust float-to-int conversion range.
Returns
-------
out : ndarray
Output array
out : ndarray (uint16)
Output array.
"""
if not isinstance(arr, np.int16):
arr = arr.copy()
Expand All @@ -191,19 +193,19 @@ def as_uint16(arr, dmin=None, dmax=None):

def remove_neg(dat, val=0.):
"""
Replace negative values in data with ``val``.
Replace negative values in data with a given value.
Parameters
----------
dat : ndarray
dat : ndarray (float)
Input data.
val : scalar
val : scalar (float)
Values to be replaced with negative values in data.
Returns
-------
out : ndarray
out : ndarray (float)
Corrected data.
"""
dat = as_float32(dat)
Expand All @@ -213,19 +215,19 @@ def remove_neg(dat, val=0.):

def remove_nan(dat, val=0.):
"""
Replace NaN values in data with ``val``.
Replace NaN values in data with a given value.
Parameters
----------
dat : ndarray
dat : ndarray (float)
Input data.
val : scalar
val : scalar (float)
Values to be replaced with NaN values in data.
Returns
-------
out : ndarray
out : ndarray (float)
Corrected data.
"""
dat = as_float32(dat)
Expand All @@ -243,13 +245,13 @@ def _add_index_to_string(string, ind, digit):
Parameters
----------
string : string
Given string.
Given string (typically a file name).
ind : scalar
The index to be added at the end of string.
ind : scalar (int)
A value index to be added at the end of string.
digit : scalar
Number of digit for the string indexing.
digit : scalar (int)
Number of digits in indexing tiff images.
Returns
-------
Expand All @@ -271,8 +273,8 @@ def _add_index_to_string(string, ind, digit):

def _suggest_new_fname(fname):
"""
Suggests a new file name with an attached (or increased) index
at the end of the file name.
Suggest new string with an attached (or increased) value indexing
at the end of a given string.
For example if "myfile.tiff" exist, it will return "myfile-1.tiff".
Expand All @@ -284,7 +286,7 @@ def _suggest_new_fname(fname):
Returns
-------
out : string
Indexed new file.
Indexed new string.
"""
ext = '.' + fname.split(".")[-1]
fname = fname.split(".")[-2]
Expand All @@ -311,11 +313,11 @@ def read_hdf5(fname, gname="/exchange/data", dtype='float32'):
Path to hdf5 file.
gname : string
Path to group where data is.
Path to the group inside hdf5 file where data is located.
Returns
-------
out : ndarray (probably)
out : ndarray mostly
Returned data.
"""
fname = os.path.abspath(fname)
Expand All @@ -331,22 +333,22 @@ def write_hdf5(data, fname, gname="exchange", overwrite=False):
Parameters
----------
data : ndarray (probably)
data : ndarray mostly
Input data.
fname : string
Path to hdf5 file without extension.
gname : string
Path to group where data is.
Path to the group inside hdf5 file where data is located.
overwrite: bool, optional
if True the existing files in the reconstruction folder will be
overwrite: bool
if True, the existing files in the reconstruction folder will be
overwritten with the new ones.
Returns
-------
out : ndarray (probably)
out : ndarray mostly
Returned data.
"""
fname += '.h5'
Expand All @@ -370,11 +372,11 @@ def read_tiff_stack(fname, span, digit, ext='tiff'):
fname : string
Path to hdf5 file.
span : list
span : list (int)
(start, end) indices of the files to read.
digit : scalar
Determines the number of digits in indexing tiff images.
digit : scalar (int)
Number of digits in indexing tiff images.
ext : string
Specifies the extension of tiff files (e.g., tiff or tif).
Expand Down Expand Up @@ -412,36 +414,34 @@ def write_tiff_stack(
digit=5, overwrite=False,
dtype='uint8', dmin=None, dmax=None):
"""
Write 3-D data to a stack of tiff files.
Write 3D data to a stack of tiff files.
Parameters
-----------
data : ndarray
3-D input data.
----------
data : 3D data (int or float)
Input data as 3D array.
fname : str, optional
Path of the output file without any extensions.
fname : string
Path of output file without extension.
id : scalar, optional
First index of the data on first dimension of the array.
axis : scalar (int)
Axis along which saving is performed.
digit : scalar, optional
Number of digit used for file indexing.
For example if 4: test_XXXX.tiff
id : scalar (int)
First index of file for saving.
axis : scalar, optional
Images are read along that axis.
digit : scalar (int)
Number of digits in indexing tiff images.
overwrite: bool, optional
if True the existing files in the reconstruction folder will be
overwrite: bool
if True, the existing files in the reconstruction folder will be
overwritten with the new ones.
dtype : bool, optional
Export data type precision.
dtype : bool
The desired data-type for saved images.
dmin, dmax : scalar, optional
User defined minimum and maximum values in the data that will be
used to scale the dataset when saving.
dmin, dmax : scalar
Minimum and maximum values in data for scaling before saving.
"""
ext = '.tiff'
fname = os.path.abspath(fname)
Expand Down

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