Dec 10, 2022 · Dec 10, 2022 · Dec 10, 2022 · Apr 5, 2023 · Apr 5, 2023 · Jun 6, 2023
diff --git a/nibabel/freesurfer/io.py b/nibabel/freesurfer/io.py
 """Read / write FreeSurfer geometry, morphometry, label, annotation formats"""
 """Read / write FreeSurfer geometry, morphometry, label, stats, annotation formats"""
 from __future__importannotations

 importgetpass
 importtime
 val=volume_info[key]
 strings.append(f'{key:6s} ={val[0]:.10g}{val[1]:.10g}{val[2]:.10g}\n'.encode())
 returnb''.join(strings)

 defread_stats_file(file_path):
 """Extracts stats from stats files except '*curv.stats' files

    Parameters
    ----------
    file_path: str, required

    Examples
    --------
    >>> stats_a2009, column_names = read_stats_file(r'lh.aparc.a2009s.stats')

    """
 withopen(file_path,'r')asf:
 forlineinf:
 ifline.startswith('# ColHeaders '):
 columns=line.split()[2:]
 break
 returnnp.genfromtxt(f,dtype=None,names=columns,encoding='utf-8')


 defread_stats_file_both_hemispheres(file_path:str):
 """Extracts stats data of both hemispheres and merges them

    Parameters
    ----------
    file_path: str, required
        Path of the stats file belong to left (lh) or right(rh) hemisphere

    Returns
    -------
    stats_both_hemispheres: ndarray
        Stats data of both hemisphers
    column_naems: ndarray
        Name of columns

    Examples
    --------
    >>> stats_a2009, column_names = read_stats_file_both_hemispheres(r'lh.aparc.a2009s.stats')

    """
 stats_left,columns_left=read_stats_file(file_path.replace('rh','lh'))
 stats_right,columns_right=read_stats_file(file_path.replace('lh','rh'))
 stats_both_hemispheres=np.concatenate((stats_left,stats_right[:,1:]),axis=1)
 column_names= [col_name+'_left'forcol_nameincolumns_left]+ [col_name+'_right'forcol_namein
 columns_right[1:]]
 returnstats_both_hemispheres,column_names
Original file line number	Diff line number	Diff line change
		@@ -1,4 +1,5 @@
		"""Read / write FreeSurfer geometry, morphometry, label, annotation formats"""
		"""Read / write FreeSurfer geometry, morphometry, label, stats, annotation formats"""
		from __future__importannotations
effigies marked this conversation as resolved. Show resolvedHide resolved

		importgetpass
		importtime
Expand DownExpand Up		@@ -617,3 +618,50 @@
		val=volume_info[key]
		strings.append(f'{key:6s} ={val[0]:.10g}{val[1]:.10g}{val[2]:.10g}\n'.encode())
		returnb''.join(strings)

		defread_stats_file(file_path):
		"""Extracts stats from stats files except '*curv.stats' files

		Parameters
		----------
		file_path: str, required

		Examples
		--------
		>>> stats_a2009, column_names = read_stats_file(r'lh.aparc.a2009s.stats')
Copy link Member effigiesDec 26, 2022 Choose a reason for hiding this comment The reason will be displayed to describe this comment to others.Learn more. If we're going to have example code, it needs to run. We could drop an example file in`nibabel/tests/data/` and access it with fromnibabel.testingimporttest_datastats_a2009=read_stats_file(test_data(fname='lh.aparc.a2009s.stats'))

		"""
		withopen(file_path,'r')asf:
		forlineinf:
		ifline.startswith('# ColHeaders '):
		columns=line.split()[2:]
		break
		returnnp.genfromtxt(f,dtype=None,names=columns,encoding='utf-8')
Check warning on line 639 in nibabel/freesurfer/io.py View check run for this annotation Codecov/ codecov/patch nibabel/freesurfer/io.py#L637-L639 `Added lines #L637 - L639 were not covered by tests`


		defread_stats_file_both_hemispheres(file_path:str):
		"""Extracts stats data of both hemispheres and merges them

		Parameters
		----------
		file_path: str, required
		Path of the stats file belong to left (lh) or right(rh) hemisphere

		Returns
		-------
		stats_both_hemispheres: ndarray
		Stats data of both hemisphers
		column_naems: ndarray
		Name of columns

		Examples
		--------
		>>> stats_a2009, column_names = read_stats_file_both_hemispheres(r'lh.aparc.a2009s.stats')

		"""
		stats_left,columns_left=read_stats_file(file_path.replace('rh','lh'))
		stats_right,columns_right=read_stats_file(file_path.replace('lh','rh'))
		stats_both_hemispheres=np.concatenate((stats_left,stats_right[:,1:]),axis=1)
Check warning on line 664 in nibabel/freesurfer/io.py View check run for this annotation Codecov/ codecov/patch nibabel/freesurfer/io.py#L663-L664 `Added lines #L663 - L664 were not covered by tests`
		column_names= [col_name+'_left'forcol_nameincolumns_left]+ [col_name+'_right'forcol_namein
		columns_right[1:]]
Comment on lines +662 to +666 Copy link Member effigiesSep 24, 2024 Choose a reason for hiding this comment The reason will be displayed to describe this comment to others.Learn more. You're no longer returning column names. I think you can usenumpy.lib.recfunctions.join_by to do what you want. I would also use the following pattern for doctests: ..testsetup:: >>>import os >>>from nibabel.testingimport get_test_data >>>cwd= os.getcwd() >>>os.chdir(get_test_data()) >>>stats_a2009= read_stats_file_both_hemispheres(r'lh.aparc.a2009s.stats') ..testcleanup:: >>>os.chdir(cwd)
		returnstats_both_hemispheres,column_names
Check warning on line 667 in nibabel/freesurfer/io.py View check run for this annotation Codecov/ codecov/patch nibabel/freesurfer/io.py#L667 `Added line #L667 was not covered by tests`