From dfed1e38d5e6b221ef681ca6cd721a734c99476c Mon Sep 17 00:00:00 2001
From: Ehsan Karimi <39439514+ehkarimi@users.noreply.github.com>
Date: Sat, 10 Dec 2022 08:03:08 -0500
Subject: [PATCH 1/4] Update io.py
there was a problem with reading the stats files
---
nibabel/freesurfer/io.py | 56 +++++++++++++++++++++++++++++++++++++++-
1 file changed, 55 insertions(+), 1 deletion(-)
diff --git a/nibabel/freesurfer/io.py b/nibabel/freesurfer/io.py
index e2f48d88eb..b7d294b120 100644
--- a/nibabel/freesurfer/io.py
+++ b/nibabel/freesurfer/io.py
@@ -1,10 +1,13 @@
-""" Read / write FreeSurfer geometry, morphometry, label, annotation formats
+""" Read / write FreeSurfer geometry, morphometry, label, stats, annotation formats
"""
+from __future__ import annotations
import warnings
import numpy as np
import getpass
import time
+import re
+import pandas as pd
from collections import OrderedDict
from ..openers import Opener
@@ -622,3 +625,54 @@ def _serialize_volume_info(volume_info):
strings.append(
f'{key:6s} = {val[0]:.10g} {val[1]:.10g} {val[2]:.10g}\n'.encode('utf-8'))
return b''.join(strings)
+
+
+class StatsFileReader:
+
+ @staticmethod
+ def read_stats_file(file_path):
+ """Extracts stats from stats files except '*curv.stats' files
+
+ Parameters
+ ----------
+ file_path: str, required
+
+ Returns
+ -------
+
+ """
+ with open(file_path, 'r') as f:
+ for line in f:
+ if re.findall(r'ColHeaders .*', line):
+ parameters = line.split()
+ break
+ f.close()
+ stats = np.loadtxt(file_path, comments='#', dtype=str)
+ df_stats = pd.DataFrame(stats, columns=parameters[2:])
+ df_stats.set_index('StructName', drop=True, inplace=True)
+ return df_stats
+
+ @staticmethod
+ def read_stats_file_both_hemispheres(file_path: str):
+ """Extracts stats data of both hemisphers and merges them
+
+ Parameters
+ ----------
+ file_path: str, required
+ Path of the stats file belong to left (lh) or right(rh) hemisphere
+
+ Returns
+ -------
+ df_both_hemispheres: pd.DataFrame
+ Stats data of both hemisphers
+
+ Examples
+ --------
+ >>> df_stats_a2009 = StatsFileReader.read_stats_file(r'lh.aparc.a2009s.stats')
+
+ """
+ df_left = StatsFileReader.read_stats_file(file_path.replace('rh', 'lh'))
+ df_right = StatsFileReader.read_stats_file(file_path.replace('lh', 'rh'))
+ df_both_hemispheres = pd.merge(df_left, df_right, suffixes=('_lh', '_rh'), how='outer', left_index=True,
+ right_index=True)
+ return df_both_hemispheres
From 84d6e047cb4e928dc15b88ad8dc277bc12c87669 Mon Sep 17 00:00:00 2001
From: Ehsan Karimi <39439514+ehkarimi@users.noreply.github.com>
Date: Sat, 10 Dec 2022 12:04:20 -0500
Subject: [PATCH 2/4] Stats file reader functions are added
---
nibabel/freesurfer/io.py | 100 +++++++++++++++++++--------------------
1 file changed, 49 insertions(+), 51 deletions(-)
diff --git a/nibabel/freesurfer/io.py b/nibabel/freesurfer/io.py
index b7d294b120..048dd3bdfa 100644
--- a/nibabel/freesurfer/io.py
+++ b/nibabel/freesurfer/io.py
@@ -6,8 +6,7 @@
import numpy as np
import getpass
import time
-import re
-import pandas as pd
+import re
from collections import OrderedDict
from ..openers import Opener
@@ -626,53 +625,52 @@ def _serialize_volume_info(volume_info):
f'{key:6s} = {val[0]:.10g} {val[1]:.10g} {val[2]:.10g}\n'.encode('utf-8'))
return b''.join(strings)
+def read_stats_file(file_path):
+ """Extracts stats from stats files except '*curv.stats' files
-class StatsFileReader:
-
- @staticmethod
- def read_stats_file(file_path):
- """Extracts stats from stats files except '*curv.stats' files
-
- Parameters
- ----------
- file_path: str, required
-
- Returns
- -------
-
- """
- with open(file_path, 'r') as f:
- for line in f:
- if re.findall(r'ColHeaders .*', line):
- parameters = line.split()
- break
- f.close()
- stats = np.loadtxt(file_path, comments='#', dtype=str)
- df_stats = pd.DataFrame(stats, columns=parameters[2:])
- df_stats.set_index('StructName', drop=True, inplace=True)
- return df_stats
-
- @staticmethod
- def read_stats_file_both_hemispheres(file_path: str):
- """Extracts stats data of both hemisphers and merges them
-
- Parameters
- ----------
- file_path: str, required
- Path of the stats file belong to left (lh) or right(rh) hemisphere
-
- Returns
- -------
- df_both_hemispheres: pd.DataFrame
- Stats data of both hemisphers
-
- Examples
- --------
- >>> df_stats_a2009 = StatsFileReader.read_stats_file(r'lh.aparc.a2009s.stats')
-
- """
- df_left = StatsFileReader.read_stats_file(file_path.replace('rh', 'lh'))
- df_right = StatsFileReader.read_stats_file(file_path.replace('lh', 'rh'))
- df_both_hemispheres = pd.merge(df_left, df_right, suffixes=('_lh', '_rh'), how='outer', left_index=True,
- right_index=True)
- return df_both_hemispheres
+ Parameters
+ ----------
+ file_path: str, required
+
+ Examples
+ --------
+ >>> stats_a2009, column_names = read_stats_file(r'lh.aparc.a2009s.stats')
+
+ """
+ with open(file_path, 'r') as f:
+ for line in f:
+ if re.findall(r'ColHeaders .*', line):
+ parameters = line.split()
+ break
+ f.close()
+ stats = np.loadtxt(file_path, comments='#', dtype=str)
+ column_names = parameters[2:]
+ return stats, column_names
+
+
+def read_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' for col_name in columns_left] + [col_name + '_right' for col_name in
+ columns_right[1:]]
+ return stats_both_hemispheres, column_names
From 8880a1ae4a2ead0cb3ff04e6ef633b4694dcbddf Mon Sep 17 00:00:00 2001
From: "Simon(Ehsan) Karimi" <39439514+simkarwin@users.noreply.github.com>
Date: Wed, 5 Apr 2023 03:53:57 -0400
Subject: [PATCH 3/4] Update nibabel/freesurfer/io.py
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
nibabel/freesurfer/io.py | 9 +++------
1 file changed, 3 insertions(+), 6 deletions(-)
diff --git a/nibabel/freesurfer/io.py b/nibabel/freesurfer/io.py
index 048dd3bdfa..bcf10ccdbd 100644
--- a/nibabel/freesurfer/io.py
+++ b/nibabel/freesurfer/io.py
@@ -639,13 +639,10 @@ def read_stats_file(file_path):
"""
with open(file_path, 'r') as f:
for line in f:
- if re.findall(r'ColHeaders .*', line):
- parameters = line.split()
+ if line.startswith('# ColHeaders '):
+ columns = line.split()[2:]
break
- f.close()
- stats = np.loadtxt(file_path, comments='#', dtype=str)
- column_names = parameters[2:]
- return stats, column_names
+ return np.genfromtxt(f, dtype=None, names=columns, encoding='utf-8')
def read_stats_file_both_hemispheres(file_path: str):
From 97107b7b8ba71e385dc39db8d57e9883050922c3 Mon Sep 17 00:00:00 2001
From: "Simon(Ehsan) Karimi" <39439514+simkarwin@users.noreply.github.com>
Date: Wed, 5 Apr 2023 03:54:29 -0400
Subject: [PATCH 4/4] Update nibabel/freesurfer/io.py
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
nibabel/freesurfer/io.py | 1 -
1 file changed, 1 deletion(-)
diff --git a/nibabel/freesurfer/io.py b/nibabel/freesurfer/io.py
index bcf10ccdbd..dda6117f5b 100644
--- a/nibabel/freesurfer/io.py
+++ b/nibabel/freesurfer/io.py
@@ -6,7 +6,6 @@
import numpy as np
import getpass
import time
-import re
from collections import OrderedDict
from ..openers import Opener