From b8bead9f3a26b981b735c831e0852c3c362cdb65 Mon Sep 17 00:00:00 2001
From: Howard Chiu <137316255+chiuhoward@users.noreply.github.com>
Date: Fri, 8 Nov 2024 22:56:11 -0800
Subject: [PATCH 1/4] Update segmentation.py

Enhancement for #14 to accommodate .tck.gz files by first unzipping them.

mapping.py also uses tractography_imap but does not check for extensions, would it matter there?
---
 AFQ/tasks/segmentation.py | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/AFQ/tasks/segmentation.py b/AFQ/tasks/segmentation.py
index 65be67ee..e8f4697a 100644
--- a/AFQ/tasks/segmentation.py
+++ b/AFQ/tasks/segmentation.py
@@ -30,6 +30,8 @@
 from dipy.stats.analysis import afq_profile
 from dipy.tracking.streamline import set_number_of_points, values_from_volume
 
+import gzip
+import shutil
 
 logger = logging.getLogger('AFQ')
 
@@ -61,6 +63,18 @@ def segment(data_imap, mapping_imap,
         trx = load_trx(streamlines, data_imap["dwi"])
         trx.streamlines._data = trx.streamlines._data.astype(np.float32)
         tg = trx.to_sft()
+    elif streamlines.endswith(".tck.gz"):
+        # uncompress tck.gz to a temporary tck:
+        temp_tck = streamlines.replace(".gz", "")
+        with gzip.open(streamlines, 'rb') as f_in:
+            with open(temp_tck, 'wb') as f_out:
+                shutil.copyfileobj(f_in, f_out)
+        # initialize stateful tractogram from tck file:
+        tg = load_tractogram(
+            temp_tck, data_imap["dwi"], Space.VOX, 
+            bbox_valid_check=False)
+        is_trx = False
+
 
     indices_to_remove, _ = tg.remove_invalid_streamlines()
     if len(indices_to_remove) > 0:

From 4b04c5dcfaf840bd1186de9ace88f81aceddfbc3 Mon Sep 17 00:00:00 2001
From: Howard Chiu <137316255+chiuhoward@users.noreply.github.com>
Date: Tue, 12 Nov 2024 00:57:00 -0800
Subject: [PATCH 2/4] Update segmentation.py

Added mkdtemp
---
 AFQ/tasks/segmentation.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/AFQ/tasks/segmentation.py b/AFQ/tasks/segmentation.py
index e8f4697a..db6a0783 100644
--- a/AFQ/tasks/segmentation.py
+++ b/AFQ/tasks/segmentation.py
@@ -32,6 +32,8 @@
 
 import gzip
 import shutil
+import os.path as op
+from tempfile import mkdtemp
 
 logger = logging.getLogger('AFQ')
 
@@ -65,7 +67,7 @@ def segment(data_imap, mapping_imap,
         tg = trx.to_sft()
     elif streamlines.endswith(".tck.gz"):
         # uncompress tck.gz to a temporary tck:
-        temp_tck = streamlines.replace(".gz", "")
+        temp_tck = op.join(mkdtemp(), streamlines.replace(".gz", ""))
         with gzip.open(streamlines, 'rb') as f_in:
             with open(temp_tck, 'wb') as f_out:
                 shutil.copyfileobj(f_in, f_out)

From 39c9396faf75c89f9854ae24911cbd071a4e8087 Mon Sep 17 00:00:00 2001
From: Howard Chiu <137316255+chiuhoward@users.noreply.github.com>
Date: Tue, 12 Nov 2024 13:47:56 -0800
Subject: [PATCH 3/4] Update segmentation.py

Print temp_tck for debugging
---
 AFQ/tasks/segmentation.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/AFQ/tasks/segmentation.py b/AFQ/tasks/segmentation.py
index db6a0783..d49342da 100644
--- a/AFQ/tasks/segmentation.py
+++ b/AFQ/tasks/segmentation.py
@@ -68,6 +68,7 @@ def segment(data_imap, mapping_imap,
     elif streamlines.endswith(".tck.gz"):
         # uncompress tck.gz to a temporary tck:
         temp_tck = op.join(mkdtemp(), streamlines.replace(".gz", ""))
+        print(temp_tck)
         with gzip.open(streamlines, 'rb') as f_in:
             with open(temp_tck, 'wb') as f_out:
                 shutil.copyfileobj(f_in, f_out)

From ef436f1d3005deeda8596e86b73ca3c3e7b4d2b2 Mon Sep 17 00:00:00 2001
From: Howard Chiu <137316255+chiuhoward@users.noreply.github.com>
Date: Wed, 13 Nov 2024 13:45:58 -0800
Subject: [PATCH 4/4] Update segmentation.py

split temp_tck path to generate relative path instead of absolute path
---
 AFQ/tasks/segmentation.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/AFQ/tasks/segmentation.py b/AFQ/tasks/segmentation.py
index d49342da..3130a02c 100644
--- a/AFQ/tasks/segmentation.py
+++ b/AFQ/tasks/segmentation.py
@@ -67,8 +67,8 @@ def segment(data_imap, mapping_imap,
         tg = trx.to_sft()
     elif streamlines.endswith(".tck.gz"):
         # uncompress tck.gz to a temporary tck:
-        temp_tck = op.join(mkdtemp(), streamlines.replace(".gz", ""))
-        print(temp_tck)
+        temp_tck = op.join(mkdtemp(), op.split(streamlines.replace(".gz", ""))[1])
+        logger.info(f"Temporary tck file created at: {temp_tck}")
         with gzip.open(streamlines, 'rb') as f_in:
             with open(temp_tck, 'wb') as f_out:
                 shutil.copyfileobj(f_in, f_out)