From a8410554bc4802b7d0db26a8e5c8ea006fcac7c0 Mon Sep 17 00:00:00 2001
From: Soichi Hayashi <hayashis@iu.edu>
Date: Sun, 27 Jan 2019 16:40:00 -0500
Subject: [PATCH 01/12] fixed a bug where tck _read() is expecting specific
 binary expression for fiber_delimiter and eof_delimiter.

---
 nibabel/streamlines/tck.py | 75 +++++++++++++++-----------------------
 1 file changed, 30 insertions(+), 45 deletions(-)

diff --git a/nibabel/streamlines/tck.py b/nibabel/streamlines/tck.py
index 31f0be0ab5..95db07d755 100644
--- a/nibabel/streamlines/tck.py
+++ b/nibabel/streamlines/tck.py
@@ -385,14 +385,9 @@ def _read(cls, fileobj, header, buffer_size=4):
             Streamline points
         """
         dtype = header["_dtype"]
-        coordinate_size = 3 * dtype.itemsize
-        # Make buffer_size an integer and a multiple of coordinate_size.
-        buffer_size = int(buffer_size * MEGABYTE)
-        buffer_size += coordinate_size - (buffer_size % coordinate_size)
 
-        # Markers for streamline end and file end
-        fiber_marker = cls.FIBER_DELIMITER.astype(dtype).tostring()
-        eof_marker = cls.EOF_DELIMITER.astype(dtype).tostring()
+        #align batch_size to be multiple of 3 within the specified buffer size
+        batch_size = int(buffer_size * MEGABYTE / dtype.itemsize / 3) * 3
 
         with Opener(fileobj) as f:
             start_position = f.tell()
@@ -401,46 +396,36 @@ def _read(cls, fileobj, header, buffer_size=4):
             f.seek(header["_offset_data"], os.SEEK_SET)
 
             eof = False
-            buffs = []
             n_streams = 0
-
+            leftover = np.empty([0,3])
             while not eof:
-                buff = bytearray(buffer_size)
-                n_read = f.readinto(buff)
-                eof = n_read != buffer_size
-                if eof:
-                    buff = buff[:n_read]
-
-                buffs.append(buff)
-
-                # Make sure we've read enough to find a streamline delimiter.
-                if fiber_marker not in buff:
-                    # If we've read the whole file, then fail.
-                    if eof:
-                        # Could have minimal buffering, and have read only the
-                        # EOF delimiter
-                        buffs = [bytearray().join(buffs)]
-                        if not buffs[0] == eof_marker:
-                            raise DataError(
-                                "Cannot find a streamline delimiter. This file"
-                                " might be corrupted.")
-                    else:
-                        # Otherwise read a bit more.
-                        continue
-
-                all_parts = bytearray().join(buffs).split(fiber_marker)
-                point_parts, buffs = all_parts[:-1], all_parts[-1:]
-                point_parts = [p for p in point_parts if p != b'']
-
-                for point_part in point_parts:
-                    # Read floats.
-                    pts = np.frombuffer(point_part, dtype=dtype)
-                    # Convert data to little-endian if needed.
-                    yield pts.astype('<f4', copy=False).reshape([-1, 3])
-
-                n_streams += len(point_parts)
-
-            if not buffs[-1] == eof_marker:
+
+                # read raw files from file
+                raw_values = np.fromfile(f.fobj, dtype, batch_size)
+                if len(raw_values) < batch_size:
+                    eof = True
+
+                # Convert raw_values into a list of little-endian tuples (for x,y,z coord)
+                coords = raw_values.astype('<f4', copy=False).reshape([-1, 3])
+
+                # find stream delimiter locations (all NaNs)
+                delims = np.where(np.all(np.isnan(coords), axis=1))[0]
+
+                # for each delimiters, yeild new streams
+                begin = 0
+                for i in range(0, len(delims)):
+                    end = delims[i]
+                    stream = np.append(leftover, coords[begin:end], axis=0)
+                    leftover = np.empty([0,3])
+                    yield stream
+                    n_streams += 1
+
+                    begin = end+1 #skip the delimiter
+
+                # the rest gets appended to the leftover
+                leftover = np.append(leftover, coords[begin:], axis=0)
+
+            if not np.all(np.isinf(leftover), axis=1):
                 raise DataError("Expecting end-of-file marker 'inf inf inf'")
 
             # In case the 'count' field was not provided.

From cd2a2b99a497b9f340f6a8091f330256d7e2a500 Mon Sep 17 00:00:00 2001
From: Soichi Hayashi <hayashis@iu.edu>
Date: Mon, 28 Jan 2019 16:56:49 -0500
Subject: [PATCH 02/12] optimized performance (now it's 4% faster than the
 original code)

---
 nibabel/streamlines/tck.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/nibabel/streamlines/tck.py b/nibabel/streamlines/tck.py
index 95db07d755..6e10e69f5e 100644
--- a/nibabel/streamlines/tck.py
+++ b/nibabel/streamlines/tck.py
@@ -397,7 +397,7 @@ def _read(cls, fileobj, header, buffer_size=4):
 
             eof = False
             n_streams = 0
-            leftover = np.empty([0,3])
+            leftover = np.empty((0,3), dtype='<f4')
             while not eof:
 
                 # read raw files from file
@@ -415,15 +415,18 @@ def _read(cls, fileobj, header, buffer_size=4):
                 begin = 0
                 for i in range(0, len(delims)):
                     end = delims[i]
-                    stream = np.append(leftover, coords[begin:end], axis=0)
-                    leftover = np.empty([0,3])
+                    if i == 0:
+                        stream = np.vstack((leftover, coords[begin:end]))
+                    else:
+                        stream = coords[begin:end]
+                    leftover = np.empty((0,3), dtype='<f4')
                     yield stream
                     n_streams += 1
 
                     begin = end+1 #skip the delimiter
 
                 # the rest gets appended to the leftover
-                leftover = np.append(leftover, coords[begin:], axis=0)
+                leftover = np.vstack((leftover, coords[begin:]))
 
             if not np.all(np.isinf(leftover), axis=1):
                 raise DataError("Expecting end-of-file marker 'inf inf inf'")

From 62c0cda85597ed228cb9672183eedf7d29d9f9a1 Mon Sep 17 00:00:00 2001
From: Soichi Hayashi <hayashis@iu.edu>
Date: Tue, 29 Jan 2019 08:47:14 -0500
Subject: [PATCH 03/12] added matlab_nan.tck, a test tck file containing NaN
 and Inf in a different binary format from the current numpy.nan and numpy.inf

---
 nibabel/tests/data/matlab_nan.tck | Bin 0 -> 1657 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 nibabel/tests/data/matlab_nan.tck

diff --git a/nibabel/tests/data/matlab_nan.tck b/nibabel/tests/data/matlab_nan.tck
new file mode 100644
index 0000000000000000000000000000000000000000..6afc9af60c5fe38a6905ba21bc63b47d721de811
GIT binary patch
literal 1657
zcmY+B3sh9)7RLt=qQixJ<l}n1I7!6nAq}7+pfP&_3l#05C=BW_&J4^jGv~~lb0!98
zm9j(>rA#udOBeA<Wh7=kgT7ZOb>;dhO>PLe#26z$95YZM?wGY&?X~t=``h1t|MvdA
zZ5L(H;#SI{-e8qDqh8j_#ST-Va)C|I%W<)bQaOX*;^jo;oS4}vm5Q_Q7Fj2oMU!L}
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zAAq&rjU^M(ZmO4Q{PDo?XfmaANImIi1vW0vAO-J?sGF)rQI2dQNjZM7PB((6VgoUB
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z`wiKgJ{FoExPh*zJ%n!>4~G7J6dyE1w2>2`L)(XDzBGpBZJrD>H}#@6E|l)<{VTlx
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literal 0
HcmV?d00001


From 8ed4acadbeb92ecfffdf0ec80f05abb2d4753049 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Wed, 30 Jan 2019 22:41:18 -0500
Subject: [PATCH 04/12] RF: Reduce concatenations further, moderate cleanups

---
 nibabel/streamlines/tck.py | 38 ++++++++++++++++++--------------------
 1 file changed, 18 insertions(+), 20 deletions(-)

diff --git a/nibabel/streamlines/tck.py b/nibabel/streamlines/tck.py
index 6e10e69f5e..847c852d31 100644
--- a/nibabel/streamlines/tck.py
+++ b/nibabel/streamlines/tck.py
@@ -386,7 +386,7 @@ def _read(cls, fileobj, header, buffer_size=4):
         """
         dtype = header["_dtype"]
 
-        #align batch_size to be multiple of 3 within the specified buffer size
+        # Align batch_size to be multiple of 3 within the specified buffer size
         batch_size = int(buffer_size * MEGABYTE / dtype.itemsize / 3) * 3
 
         with Opener(fileobj) as f:
@@ -397,7 +397,7 @@ def _read(cls, fileobj, header, buffer_size=4):
 
             eof = False
             n_streams = 0
-            leftover = np.empty((0,3), dtype='<f4')
+            leftover = np.empty((0, 3), dtype='<f4')
             while not eof:
 
                 # read raw files from file
@@ -405,30 +405,28 @@ def _read(cls, fileobj, header, buffer_size=4):
                 if len(raw_values) < batch_size:
                     eof = True
 
-                # Convert raw_values into a list of little-endian tuples (for x,y,z coord)
-                coords = raw_values.astype('<f4', copy=False).reshape([-1, 3])
+                # Convert raw_values into a list of little-endian triples (for x,y,z coord)
+                coords = raw_values.astype('<f4', copy=False).reshape((-1, 3))
 
-                # find stream delimiter locations (all NaNs)
-                delims = np.where(np.all(np.isnan(coords), axis=1))[0]
+                # Find stream delimiter locations (all NaNs)
+                delims = np.where(np.isnan(coords).all(axis=1))[0]
+
+                if leftover.size:
+                    delims += leftover.shape[0]
+                    coords = np.vstack((leftover, coords))
 
-                # for each delimiters, yeild new streams
                 begin = 0
-                for i in range(0, len(delims)):
-                    end = delims[i]
-                    if i == 0:
-                        stream = np.vstack((leftover, coords[begin:end]))
-                    else:
-                        stream = coords[begin:end]
-                    leftover = np.empty((0,3), dtype='<f4')
-                    yield stream
-                    n_streams += 1
-
-                    begin = end+1 #skip the delimiter
+                for delim in delims:
+                    pts = coords[begin:delim]
+                    if pts.size:
+                        yield coords[begin:delim]
+                        n_streams += 1
+                    begin = delim + 1
 
                 # the rest gets appended to the leftover
-                leftover = np.vstack((leftover, coords[begin:]))
+                leftover = coords[begin:]
 
-            if not np.all(np.isinf(leftover), axis=1):
+            if not np.isinf(leftover).all():
                 raise DataError("Expecting end-of-file marker 'inf inf inf'")
 
             # In case the 'count' field was not provided.

From 74c3410678df87159392cea100606e281191da46 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Wed, 30 Jan 2019 23:06:12 -0500
Subject: [PATCH 05/12] FIX: Return to bytearray/frombuffer approach

---
 nibabel/streamlines/tck.py | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/nibabel/streamlines/tck.py b/nibabel/streamlines/tck.py
index 847c852d31..53fb26ee13 100644
--- a/nibabel/streamlines/tck.py
+++ b/nibabel/streamlines/tck.py
@@ -386,8 +386,10 @@ def _read(cls, fileobj, header, buffer_size=4):
         """
         dtype = header["_dtype"]
 
-        # Align batch_size to be multiple of 3 within the specified buffer size
-        batch_size = int(buffer_size * MEGABYTE / dtype.itemsize / 3) * 3
+        coordinate_size = 3 * dtype.itemsize
+        # Make buffer_size an integer and a multiple of coordinate_size.
+        buffer_size = int(buffer_size * MEGABYTE)
+        buffer_size += coordinate_size - (buffer_size % coordinate_size)
 
         with Opener(fileobj) as f:
             start_position = f.tell()
@@ -399,11 +401,14 @@ def _read(cls, fileobj, header, buffer_size=4):
             n_streams = 0
             leftover = np.empty((0, 3), dtype='<f4')
             while not eof:
+                buff = bytearray(buffer_size)
+                n_read = f.readinto(buff)
+                eof = n_read != buffer_size
+                if eof:
+                    buff = buff[:n_read]
 
                 # read raw files from file
-                raw_values = np.fromfile(f.fobj, dtype, batch_size)
-                if len(raw_values) < batch_size:
-                    eof = True
+                raw_values = np.frombuffer(buff, dtype=dtype)
 
                 # Convert raw_values into a list of little-endian triples (for x,y,z coord)
                 coords = raw_values.astype('<f4', copy=False).reshape((-1, 3))

From 10ae9bcfe727678fd395325d1a65f8b0da783c99 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Wed, 30 Jan 2019 23:06:46 -0500
Subject: [PATCH 06/12] FIX: Check final delimiter is ONLY infs

---
 nibabel/streamlines/tck.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nibabel/streamlines/tck.py b/nibabel/streamlines/tck.py
index 53fb26ee13..17e41989a8 100644
--- a/nibabel/streamlines/tck.py
+++ b/nibabel/streamlines/tck.py
@@ -431,7 +431,7 @@ def _read(cls, fileobj, header, buffer_size=4):
                 # the rest gets appended to the leftover
                 leftover = coords[begin:]
 
-            if not np.isinf(leftover).all():
+            if not (leftover.shape == (1, 3) and np.isinf(leftover).all()):
                 raise DataError("Expecting end-of-file marker 'inf inf inf'")
 
             # In case the 'count' field was not provided.

From 0a75431a96c47e809a414e62eda0a3dce887a62b Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Wed, 30 Jan 2019 23:16:56 -0500
Subject: [PATCH 07/12] TEST: Simple load test for matlab_nan.tck

---
 nibabel/streamlines/tests/test_tck.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/nibabel/streamlines/tests/test_tck.py b/nibabel/streamlines/tests/test_tck.py
index f5752bbe8b..ad16b52754 100644
--- a/nibabel/streamlines/tests/test_tck.py
+++ b/nibabel/streamlines/tests/test_tck.py
@@ -32,6 +32,7 @@ def setup():
                                                 "simple_big_endian.tck")
     # standard.tck contains only streamlines
     DATA['standard_tck_fname'] = pjoin(data_path, "standard.tck")
+    DATA['matlab_nan_tck_fname'] = pjoin(data_path, "matlab_nan.tck")
 
     DATA['streamlines'] = [np.arange(1 * 3, dtype="f4").reshape((1, 3)),
                            np.arange(2 * 3, dtype="f4").reshape((2, 3)),
@@ -64,6 +65,13 @@ def test_load_simple_file(self):
         tck = TckFile(tractogram, header=hdr)
         assert_tractogram_equal(tck.tractogram, DATA['simple_tractogram'])
 
+    def test_load_matlab_nan_file(self):
+        for lazy_load in [False, True]:
+            tck = TckFile.load(DATA['matlab_nan_tck_fname'], lazy_load=lazy_load)
+            streamlines = list(tck.tractogram.streamlines)
+            assert_equal(len(streamlines), 1)
+            assert_equal(streamlines[0].shape, (108, 3))
+
     def test_writeable_data(self):
         data = DATA['simple_tractogram']
         for key in ('simple_tck_fname', 'simple_tck_big_endian_fname'):

From 676df4d11983ab7c0021f7f3d520e5acbac9c616 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Wed, 30 Jan 2019 23:29:17 -0500
Subject: [PATCH 08/12] STY: Reduce diff

---
 nibabel/streamlines/tck.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/nibabel/streamlines/tck.py b/nibabel/streamlines/tck.py
index 17e41989a8..cb9994a53c 100644
--- a/nibabel/streamlines/tck.py
+++ b/nibabel/streamlines/tck.py
@@ -385,7 +385,6 @@ def _read(cls, fileobj, header, buffer_size=4):
             Streamline points
         """
         dtype = header["_dtype"]
-
         coordinate_size = 3 * dtype.itemsize
         # Make buffer_size an integer and a multiple of coordinate_size.
         buffer_size = int(buffer_size * MEGABYTE)
@@ -398,8 +397,9 @@ def _read(cls, fileobj, header, buffer_size=4):
             f.seek(header["_offset_data"], os.SEEK_SET)
 
             eof = False
-            n_streams = 0
             leftover = np.empty((0, 3), dtype='<f4')
+            n_streams = 0
+
             while not eof:
                 buff = bytearray(buffer_size)
                 n_read = f.readinto(buff)
@@ -407,7 +407,6 @@ def _read(cls, fileobj, header, buffer_size=4):
                 if eof:
                     buff = buff[:n_read]
 
-                # read raw files from file
                 raw_values = np.frombuffer(buff, dtype=dtype)
 
                 # Convert raw_values into a list of little-endian triples (for x,y,z coord)
@@ -416,6 +415,7 @@ def _read(cls, fileobj, header, buffer_size=4):
                 # Find stream delimiter locations (all NaNs)
                 delims = np.where(np.isnan(coords).all(axis=1))[0]
 
+                # Recover leftovers, which can't have delimiters in them
                 if leftover.size:
                     delims += leftover.shape[0]
                     coords = np.vstack((leftover, coords))
@@ -428,7 +428,7 @@ def _read(cls, fileobj, header, buffer_size=4):
                         n_streams += 1
                     begin = delim + 1
 
-                # the rest gets appended to the leftover
+                # The rest gets appended to the leftover
                 leftover = coords[begin:]
 
             if not (leftover.shape == (1, 3) and np.isinf(leftover).all()):

From 4e1cab25ccc502d08e922505a8782b776e044c78 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Wed, 30 Jan 2019 23:43:34 -0500
Subject: [PATCH 09/12] RF: Restore missing streamline delimiter error

---
 nibabel/streamlines/tck.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/nibabel/streamlines/tck.py b/nibabel/streamlines/tck.py
index cb9994a53c..fcc39f1428 100644
--- a/nibabel/streamlines/tck.py
+++ b/nibabel/streamlines/tck.py
@@ -432,7 +432,11 @@ def _read(cls, fileobj, header, buffer_size=4):
                 leftover = coords[begin:]
 
             if not (leftover.shape == (1, 3) and np.isinf(leftover).all()):
-                raise DataError("Expecting end-of-file marker 'inf inf inf'")
+                if n_streams == 0:
+                    msg = "Cannot find a streamline delimiter. This file might be corrupted."
+                else:
+                    msg = "Expecting end-of-file marker 'inf inf inf'"
+                raise DataError(msg)
 
             # In case the 'count' field was not provided.
             header[Field.NB_STREAMLINES] = n_streams

From 196f13afe4b082b61e1c9cf7fedb8a9400518a01 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Wed, 30 Jan 2019 23:49:30 -0500
Subject: [PATCH 10/12] STY: Pacify flake8

---
 nibabel/cifti2/cifti2.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nibabel/cifti2/cifti2.py b/nibabel/cifti2/cifti2.py
index 0ffe45a169..67dab1d0c2 100644
--- a/nibabel/cifti2/cifti2.py
+++ b/nibabel/cifti2/cifti2.py
@@ -287,7 +287,7 @@ def rgba(self):
         return (self.red, self.green, self.blue, self.alpha)
 
     def _to_xml_element(self):
-        if self.label is '':
+        if self.label == '':
             raise Cifti2HeaderError('Label needs a name')
         try:
             v = int(self.key)

From bac19880f2e3e9fdcd54b454f1aa1455adb07bd3 Mon Sep 17 00:00:00 2001
From: Soichi Hayashi <hayashis@iu.edu>
Date: Mon, 4 Feb 2019 00:05:22 -0500
Subject: [PATCH 11/12] reapplied @MarcCote's suggestion.

---
 nibabel/streamlines/tck.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nibabel/streamlines/tck.py b/nibabel/streamlines/tck.py
index fcc39f1428..2fe8ef4651 100644
--- a/nibabel/streamlines/tck.py
+++ b/nibabel/streamlines/tck.py
@@ -424,7 +424,7 @@ def _read(cls, fileobj, header, buffer_size=4):
                 for delim in delims:
                     pts = coords[begin:delim]
                     if pts.size:
-                        yield coords[begin:delim]
+                        yield pts
                         n_streams += 1
                     begin = delim + 1
 

From 486bbb2160c73ab616867bda366540753c4290fa Mon Sep 17 00:00:00 2001
From: Soichi Hayashi <hayashis@iu.edu>
Date: Mon, 4 Feb 2019 08:19:03 -0500
Subject: [PATCH 12/12] applied another @MarcCote suggestion

---
 nibabel/streamlines/tck.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nibabel/streamlines/tck.py b/nibabel/streamlines/tck.py
index 2fe8ef4651..9b1888ebba 100644
--- a/nibabel/streamlines/tck.py
+++ b/nibabel/streamlines/tck.py
@@ -428,7 +428,7 @@ def _read(cls, fileobj, header, buffer_size=4):
                         n_streams += 1
                     begin = delim + 1
 
-                # The rest gets appended to the leftover
+                # The rest becomes the new leftover.
                 leftover = coords[begin:]
 
             if not (leftover.shape == (1, 3) and np.isinf(leftover).all()):