Tests for tomo motioncorr and ctf

src/cryoemservices/util/tomo_output_files.py

@@ -274,7 +274,6 @@ def _ctffind_output_files(
         ),
         str(relion_options.defocus),
         str(input_file),
-        str(stage_tilt_angle),
         str(output_file.with_suffix(".ctf")) + ":mrc",
         ctf_results[1],
         ctf_results[2],
@@ -299,7 +298,6 @@ def _ctffind_output_files(
                 "MicrographPreExposure",
                 "TomoNominalDefocus",
                 "MicrographName",
-                "TomoNominalTiltAxisAngle",
                 "CtfImage",
                 "DefocusU",
                 "DefocusV",

tests/services/test_node_creator.py

@@ -1072,9 +1072,155 @@ def test_node_creator_import_tomo(mock_environment, offline_transport, tmp_path)
     ]
 
 
+@pytest.mark.skipif(sys.platform == "win32", reason="does not run on windows")
+def test_node_creator_motioncorr_tomo(mock_environment, offline_transport, tmp_path):
+    """
+    Send a test message to the node creator for
+    relion.motioncorr.own
+    """
+    job_dir = "MotionCorr/job002"
+    input_file = f"{tmp_path}/Import/job001/Movies/Position_1_2_001_1.50_fractions.tiff"
+    output_file = tmp_path / job_dir / "Movies/Position_1_2_001_1.50_fractions.mrc"
+    relion_options = RelionServiceOptions()
+
+    # .Nodes directory doesn't get made by this job
+    (tmp_path / ".Nodes").mkdir()
+
+    setup_and_run_node_creation(
+        mock_environment,
+        relion_options,
+        offline_transport,
+        tmp_path,
+        job_dir,
+        "relion.motioncorr.own",
+        input_file,
+        output_file,
+        results={"total_motion": "10", "early_motion": "4", "late_motion": "6"},
+        experiment_type="tomography",
+    )
+
+    # Check the output file structure
+    assert (tmp_path / job_dir / "corrected_tilt_series.star").exists()
+    tilt_series_file = cif.read_file(
+        str(tmp_path / job_dir / "corrected_tilt_series.star")
+    )
+
+    global_block = tilt_series_file.find_block("global")
+    assert list(global_block.find_loop("_rlnTomoName")) == ["Position_1_2"]
+    assert list(global_block.find_loop("_rlnTomoTiltSeriesStarFile")) == [
+        f"{job_dir}/tilt_series/Position_1_2.star"
+    ]
+
+    assert (tmp_path / job_dir / "tilt_series/Position_1_2.star").exists()
+    tilts_file = cif.read_file(
+        str(tmp_path / job_dir / "tilt_series/Position_1_2.star")
+    )
+
+    tilts_block = tilts_file.sole_block()
+    assert list(tilts_block.find_loop("_rlnMicrographMovieName")) == [
+        "Import/job001/Movies/Position_1_2_001_1.50_fractions.tiff"
+    ]
+    assert list(tilts_block.find_loop("_rlnTomoTiltMovieFrameCount")) == [
+        str(relion_options.frame_count)
+    ]
+    assert list(tilts_block.find_loop("_rlnTomoNominalStageTiltAngle")) == ["1.50"]
+    assert list(tilts_block.find_loop("_rlnTomoNominalTiltAxisAngle")) == [
+        str(relion_options.tilt_axis_angle)
+    ]
+    assert list(tilts_block.find_loop("_rlnMicrographPreExposure")) == ["12.77"]
+    assert list(tilts_block.find_loop("_rlnTomoNominalDefocus")) == [
+        str(relion_options.defocus)
+    ]
+    assert list(tilts_block.find_loop("_rlnMicrographName")) == [
+        f"{job_dir}/Movies/Position_1_2_001_1.50_fractions.mrc"
+    ]
+    assert list(tilts_block.find_loop("_rlnMicrographMetadata")) == [
+        f"{job_dir}/Movies/Position_1_2_001_1.50_fractions.star"
+    ]
+    assert list(tilts_block.find_loop("_rlnAccumMotionTotal")) == ["10"]
+    assert list(tilts_block.find_loop("_rlnAccumMotionEarly")) == ["4"]
+    assert list(tilts_block.find_loop("_rlnAccumMotionLate")) == ["6"]
+
+
+@pytest.mark.skipif(sys.platform == "win32", reason="does not run on windows")
+def test_node_creator_ctffind_tomo(mock_environment, offline_transport, tmp_path):
+    """
+    Send a test message to the node creator for
+    relion.ctffind.ctffind4
+    """
+    job_dir = "CtfFind/job003"
+    input_file = (
+        f"{tmp_path}/MotionCorr/job002/Movies/Position_1_2_001_1.50_fractions.mrc"
+    )
+    output_file = tmp_path / job_dir / "Movies/Position_1_2_001_1.50_fractions.ctf"
+    relion_options = RelionServiceOptions()
+
+    output_file.parent.mkdir(parents=True)
+    with open(output_file.with_suffix(".txt"), "w") as f:
+        f.write("0.0 1.0 2.0 3.0 4.0 5.0 6.0")
+    with open(f"{output_file.with_suffix('')}_avrot.txt", "w") as f:
+        f.write(
+            "header\nheader\nheader\nheader\nheader\n0.24 0.26 0.27 0.29\n1 2 3 4\n"
+        )
+
+    # .Nodes directory doesn't get made by this job
+    (tmp_path / ".Nodes").mkdir()
+
+    setup_and_run_node_creation(
+        mock_environment,
+        relion_options,
+        offline_transport,
+        tmp_path,
+        job_dir,
+        "relion.ctffind.ctffind4",
+        input_file,
+        output_file,
+        experiment_type="tomography",
+    )
+
+    # Check the output file structure
+    assert (tmp_path / job_dir / "tilt_series_ctf.star").exists()
+    tilt_series_file = cif.read_file(str(tmp_path / job_dir / "tilt_series_ctf.star"))
+
+    global_block = tilt_series_file.find_block("global")
+    assert list(global_block.find_loop("_rlnTomoName")) == ["Position_1_2"]
+    assert list(global_block.find_loop("_rlnTomoTiltSeriesStarFile")) == [
+        f"{job_dir}/tilt_series/Position_1_2.star"
+    ]
+
+    assert (tmp_path / job_dir / "tilt_series/Position_1_2.star").exists()
+    tilts_file = cif.read_file(
+        str(tmp_path / job_dir / "tilt_series/Position_1_2.star")
+    )
+
+    tilts_block = tilts_file.sole_block()
+    assert list(tilts_block.find_loop("_rlnTomoTiltMovieFrameCount")) == [
+        str(relion_options.frame_count)
+    ]
+    assert list(tilts_block.find_loop("_rlnTomoNominalStageTiltAngle")) == ["1.50"]
+    assert list(tilts_block.find_loop("_rlnTomoNominalTiltAxisAngle")) == [
+        str(relion_options.tilt_axis_angle)
+    ]
+    assert list(tilts_block.find_loop("_rlnMicrographPreExposure")) == ["12.77"]
+    assert list(tilts_block.find_loop("_rlnTomoNominalDefocus")) == [
+        str(relion_options.defocus)
+    ]
+    assert list(tilts_block.find_loop("_rlnMicrographName")) == [
+        "MotionCorr/job002/Movies/Position_1_2_001_1.50_fractions.mrc"
+    ]
+    assert list(tilts_block.find_loop("_rlnCtfImage")) == [
+        f"{job_dir}/Movies/Position_1_2_001_1.50_fractions.ctf:mrc"
+    ]
+    assert list(tilts_block.find_loop("_rlnDefocusU")) == ["1.0"]
+    assert list(tilts_block.find_loop("_rlnDefocusV")) == ["2.0"]
+    assert list(tilts_block.find_loop("_rlnCtfAstigmatism")) == ["1.0"]
+    assert list(tilts_block.find_loop("_rlnDefocusAngle")) == ["3.0"]
+    assert list(tilts_block.find_loop("_rlnCtfFigureOfMerit")) == ["5.0"]
+    assert list(tilts_block.find_loop("_rlnCtfMaxResolution")) == ["6.0"]
+    assert list(tilts_block.find_loop("_rlnCtfIceRingDensity")) == ["5.0"]
+
+
 # Still to do:
-# "relion.motioncorr.own"
-# "relion.ctffind.ctffind4"
 # "relion.excludetilts"
 # "relion.aligntiltseries"
 # "relion.reconstructtomograms"