From e0c57a8e2dd3db6a28a4ae744151ffcf4ad50ae8 Mon Sep 17 00:00:00 2001
From: McHaillet <martenchaillet@gmail.com>
Date: Wed, 14 Aug 2024 12:54:07 +0200
Subject: [PATCH 1/3] fix: starfile write as dict so blocks are saved with
 _data_particles

---
 src/pytom_tm/entry_points.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/pytom_tm/entry_points.py b/src/pytom_tm/entry_points.py
index d565ecab..fd6c28c0 100644
--- a/src/pytom_tm/entry_points.py
+++ b/src/pytom_tm/entry_points.py
@@ -548,7 +548,9 @@ def extract_candidates(argv=None):
 
     # write out as a RELION type starfile
     starfile.write(
-        df, job.output_dir.joinpath(f"{job.tomo_id}_particles.star"), overwrite=True
+        {"particles": df},
+        job.output_dir.joinpath(f"{job.tomo_id}_particles.star"),
+        overwrite=True,
     )
 
 
@@ -1007,5 +1009,7 @@ def merge_stars(argv=None):
     dataframes = [starfile.read(f) for f in files]
 
     starfile.write(
-        pd.concat(dataframes, ignore_index=True), args.output_file, overwrite=True
+        {"particles": pd.concat(dataframes, ignore_index=True)},
+        args.output_file,
+        overwrite=True,
     )

From ddd53afc0b97143eed6c86750677bab22f27a410 Mon Sep 17 00:00:00 2001
From: McHaillet <martenchaillet@gmail.com>
Date: Wed, 14 Aug 2024 12:56:59 +0200
Subject: [PATCH 2/3] fix: change rlnDetectorPixelSize to
 rlnTomoTiltSeriesPixelSize for relion5 compatibility

---
 src/pytom_tm/extract.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/pytom_tm/extract.py b/src/pytom_tm/extract.py
index 61f40939..2c628f12 100644
--- a/src/pytom_tm/extract.py
+++ b/src/pytom_tm/extract.py
@@ -346,6 +346,7 @@ def extract_particles(
             "rlnCoordinateY": "rlnCenteredCoordinateYAngst",
             "rlnCoordinateZ": "rlnCenteredCoordinateZAngst",
             "rlnMicrographName": "rlnTomoName",
+            "rlnDetectorPixelSize": "rlnTomoTiltSeriesPixelSize",
         }
         output = output.rename(columns=column_change)
 

From 2beb502deb8496facc97d4065903754fa629d56e Mon Sep 17 00:00:00 2001
From: McHaillet <martenchaillet@gmail.com>
Date: Wed, 14 Aug 2024 12:59:17 +0200
Subject: [PATCH 3/3] add: make sure new column name is also checked in tests

---
 tests/test_tmjob.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/test_tmjob.py b/tests/test_tmjob.py
index 9db731ec..902c1e6b 100644
--- a/tests/test_tmjob.py
+++ b/tests/test_tmjob.py
@@ -631,6 +631,7 @@ def test_extraction(self):
             "rlnCenteredCoordinateYAngst",
             "rlnCenteredCoordinateZAngst",
             "rlnTomoName",
+            "rlnTomoTiltSeriesPixelSize",
         ):
             self.assertTrue(
                 column in df_rel5.columns,