Handling for the case where users enter their own tomogram names (#309)

Author: stephen-riggs

src/murfey/client/contexts/tomo.py

@@ -87,7 +87,7 @@ def _get_tilt_series_v5_12(p: Path) -> str:
     angle_idx = _find_angle_index(split_name)
     if split_name[angle_idx - 2].isnumeric():
         return split_name[angle_idx - 2]
-    return "0"
+    return ""
 
 
 def _get_tilt_angle_v5_12(p: Path) -> str:
@@ -119,14 +119,10 @@ def _get_tilt_tag_v5_12(p: Path) -> str:
 }
 
 
-def _construct_tilt_series_name(
-    tilt_tag: str, tilt_series: str, file_path: Path
-) -> str:
-    if tilt_tag:
-        if f"{tilt_tag}_{tilt_series}" in file_path.name:
-            return f"{tilt_tag}_{tilt_series}"
-        return f"{tilt_tag}{tilt_series}"
-    return tilt_series
+def _construct_tilt_series_name(file_path: Path) -> str:
+    # Assuming files end with _{tiltnumber}_{angle}_{date}_{time}_{fractions}.{suffix}
+    split_name = file_path.name.split("_")
+    return "_".join(split_name[:-5])
 
 
 def _midpoint(angles: List[float]) -> int:
@@ -397,18 +393,13 @@ def _add_tilt(
         if not self._extract_tilt_tag:
             self._extract_tilt_tag = extract_tilt_tag
         try:
-            tilt_series_num = extract_tilt_series(file_path)
             tilt_angle = extract_tilt_angle(file_path)
-            tilt_tag = extract_tilt_tag(file_path)
             try:
-                float(tilt_series_num)
                 float(tilt_angle)
             except ValueError:
-                logger.error(f"whoops, {tilt_series_num}, {tilt_angle}")
+                logger.error(f"whoops, {tilt_angle}")
                 return []
-            tilt_series = _construct_tilt_series_name(
-                tilt_tag, tilt_series_num, file_path
-            )
+            tilt_series = _construct_tilt_series_name(file_path)
 
         except Exception:
             logger.debug(
@@ -557,11 +548,8 @@ def _add_tilt(
 
         res = []
         if self._last_transferred_file:
-            last_tilt_series = (
-                f"{extract_tilt_tag(self._last_transferred_file)}_{extract_tilt_series(self._last_transferred_file)}"
-                if extract_tilt_tag(self._last_transferred_file)
-                else extract_tilt_series(self._last_transferred_file)
-            )
+            last_tilt_series = _construct_tilt_series_name(self._last_transferred_file)
+
             last_tilt_angle = extract_tilt_angle(self._last_transferred_file)
             self._last_transferred_file = file_path
             if (
@@ -740,9 +728,7 @@ def _add_tomo_tilt(
                 tilt_info_extraction = tomo_tilt_info["5.7"]
         else:
             tilt_info_extraction = tomo_tilt_info["5.7"]
-        tilt_tag = tilt_info_extraction.tag(file_path)
-        tilt_series_num = tilt_info_extraction.series(file_path)
-        tilt_series = _construct_tilt_series_name(tilt_tag, tilt_series_num, file_path)
+        tilt_series = _construct_tilt_series_name(file_path)
         return self._add_tilt(
             file_path,
             tilt_info_extraction.series,

tests/client/test_context.py

@@ -17,30 +17,33 @@ def test_tomography_context_initialisation_for_tomo(tmp_path):
 @patch("requests.get")
 @patch("requests.post")
 def test_tomography_context_add_tomo_tilt(mock_post, mock_get, tmp_path):
+    mock_post().status_code = 200
+
     env = MurfeyInstanceEnvironment(
         url=urlparse("http://localhost:8000"),
         client_id=0,
         sources=[tmp_path],
         default_destinations={tmp_path: str(tmp_path)},
     )
     context = TomographyContext("tomo", tmp_path)
-    (tmp_path / "Position_1_[30.0]_fractions.tiff").touch()
+    (tmp_path / "Position_1_001_[30.0]_date_time_fractions.tiff").touch()
     context.post_transfer(
-        tmp_path / "Position_1_[30.0]_fractions.tiff",
+        tmp_path / "Position_1_001_[30.0]_date_time_fractions.tiff",
         role="detector",
         required_position_files=[],
         required_strings=["fractions"],
         environment=env,
     )
     assert context._tilt_series == {
-        "Position_1": [tmp_path / "Position_1_[30.0]_fractions.tiff"]
+        "Position_1": [tmp_path / "Position_1_001_[30.0]_date_time_fractions.tiff"]
     }
     assert (
-        context._last_transferred_file == tmp_path / "Position_1_[30.0]_fractions.tiff"
+        context._last_transferred_file
+        == tmp_path / "Position_1_001_[30.0]_date_time_fractions.tiff"
     )
-    (tmp_path / "Position_1_[-30.0]_fractions.tiff").touch()
+    (tmp_path / "Position_1_002_[-30.0]_date_time_fractions.tiff").touch()
     context.post_transfer(
-        tmp_path / "Position_1_[-30.0]_fractions.tiff",
+        tmp_path / "Position_1_002_[-30.0]_date_time_fractions.tiff",
         role="detector",
         required_position_files=[],
         required_strings=["fractions"],
@@ -61,9 +64,9 @@ def test_tomography_context_add_tomo_tilt(mock_post, mock_get, tmp_path):
     assert context._completed_tilt_series == ["Position_1"]
 
     # Start Position_2, this is not complete
-    (tmp_path / "Position_2_[30.0]_fractions.tiff").touch()
+    (tmp_path / "Position_2_002_[30.0]_date_time_fractions.tiff").touch()
     context.post_transfer(
-        tmp_path / "Position_2_[30.0]_fractions.tiff",
+        tmp_path / "Position_2_002_[30.0]_date_time_fractions.tiff",
         role="detector",
         required_position_files=[],
         required_strings=["fractions"],
@@ -76,60 +79,63 @@ def test_tomography_context_add_tomo_tilt(mock_post, mock_get, tmp_path):
 @patch("requests.get")
 @patch("requests.post")
 def test_tomography_context_add_tomo_tilt_out_of_order(mock_post, mock_get, tmp_path):
+    mock_post().status_code = 200
+
     env = MurfeyInstanceEnvironment(
         url=urlparse("http://localhost:8000"),
         client_id=0,
         sources=[tmp_path],
         default_destinations={tmp_path: str(tmp_path)},
     )
     context = TomographyContext("tomo", tmp_path)
-    (tmp_path / "Position_1_[30.0]_fractions.tiff").touch()
+    (tmp_path / "Position_1_001_[30.0]_date_time_fractions.tiff").touch()
     context.post_transfer(
-        tmp_path / "Position_1_[30.0]_fractions.tiff",
+        tmp_path / "Position_1_001_[30.0]_date_time_fractions.tiff",
         role="detector",
         required_position_files=[],
         required_strings=["fractions"],
         environment=env,
     )
     assert context._tilt_series == {
-        "Position_1": [tmp_path / "Position_1_[30.0]_fractions.tiff"]
+        "Position_1": [tmp_path / "Position_1_001_[30.0]_date_time_fractions.tiff"]
     }
     assert (
-        context._last_transferred_file == tmp_path / "Position_1_[30.0]_fractions.tiff"
+        context._last_transferred_file
+        == tmp_path / "Position_1_001_[30.0]_date_time_fractions.tiff"
     )
-    (tmp_path / "Position_1_[-30.0]_fractions.tiff").touch()
+    (tmp_path / "Position_1_002_[-30.0]_date_time_fractions.tiff").touch()
     context.post_transfer(
-        tmp_path / "Position_1_[-30.0]_fractions.tiff",
+        tmp_path / "Position_1_002_[-30.0]_date_time_fractions.tiff",
         role="detector",
         required_position_files=[],
         required_strings=["fractions"],
         environment=env,
     )
     assert not context._completed_tilt_series
-    (tmp_path / "Position_2_[-30.0]_fractions.tiff").touch()
+    (tmp_path / "Position_2_002_[-30.0]_date_time_fractions.tiff").touch()
     context.post_transfer(
-        tmp_path / "Position_2_[-30.0]_fractions.tiff",
+        tmp_path / "Position_2_002_[-30.0]_date_time_fractions.tiff",
         role="detector",
         required_position_files=[],
         required_strings=["fractions"],
         environment=env,
     )
     assert len(context._tilt_series.values()) == 2
     assert not context._completed_tilt_series
-    (tmp_path / "Position_2_[30.0]_fractions.tiff").touch()
+    (tmp_path / "Position_2_001_[30.0]_date_time_fractions.tiff").touch()
     context.post_transfer(
-        tmp_path / "Position_2_[30.0]_fractions.tiff",
+        tmp_path / "Position_2_001_[30.0]_date_time_fractions.tiff",
         role="detector",
         required_position_files=[],
         required_strings=["fractions"],
         environment=env,
     )
     assert len(context._tilt_series.values()) == 2
     assert not context._completed_tilt_series
-    (tmp_path / "Position_3_[30.0]_fractions.tiff").touch()
-    (tmp_path / "Position_3_[-30.0]_fractions.tiff").touch()
+    (tmp_path / "Position_3_001_[30.0]_date_time_fractions.tiff").touch()
+    (tmp_path / "Position_3_002_[-30.0]_date_time_fractions.tiff").touch()
     context.post_transfer(
-        tmp_path / "Position_3_[-30.0]_fractions.tiff",
+        tmp_path / "Position_3_002_[-30.0]_date_time_fractions.tiff",
         role="detector",
         required_position_files=[],
         required_strings=["fractions"],
@@ -166,30 +172,33 @@ def test_tomography_context_add_tomo_tilt_out_of_order(mock_post, mock_get, tmp_
 @patch("requests.get")
 @patch("requests.post")
 def test_tomography_context_add_tomo_tilt_delayed_tilt(mock_post, mock_get, tmp_path):
+    mock_post().status_code = 200
+
     env = MurfeyInstanceEnvironment(
         url=urlparse("http://localhost:8000"),
         client_id=0,
         sources=[tmp_path],
         default_destinations={tmp_path: str(tmp_path)},
     )
     context = TomographyContext("tomo", tmp_path)
-    (tmp_path / "Position_1_[30.0]_fractions.tiff").touch()
+    (tmp_path / "Position_1_001_[30.0]_date_time_fractions.tiff").touch()
     context.post_transfer(
-        tmp_path / "Position_1_[30.0]_fractions.tiff",
+        tmp_path / "Position_1_001_[30.0]_date_time_fractions.tiff",
         role="detector",
         required_position_files=[],
         required_strings=["fractions"],
         environment=env,
     )
     assert context._tilt_series == {
-        "Position_1": [tmp_path / "Position_1_[30.0]_fractions.tiff"]
+        "Position_1": [tmp_path / "Position_1_001_[30.0]_date_time_fractions.tiff"]
     }
     assert (
-        context._last_transferred_file == tmp_path / "Position_1_[30.0]_fractions.tiff"
+        context._last_transferred_file
+        == tmp_path / "Position_1_001_[30.0]_date_time_fractions.tiff"
     )
-    (tmp_path / "Position_1_[-30.0]_fractions.tiff").touch()
+    (tmp_path / "Position_1_002_[-30.0]_date_time_fractions.tiff").touch()
     context.post_transfer(
-        tmp_path / "Position_1_[-30.0]_fractions.tiff",
+        tmp_path / "Position_1_002_[-30.0]_date_time_fractions.tiff",
         role="detector",
         required_position_files=[],
         required_strings=["fractions"],
@@ -210,9 +219,9 @@ def test_tomography_context_add_tomo_tilt_delayed_tilt(mock_post, mock_get, tmp_
     assert not context._completed_tilt_series
 
     # Now add the tilt which completes the series
-    (tmp_path / "Position_1_[60.0]_fractions.tiff").touch()
+    (tmp_path / "Position_1_003_[60.0]_data_time_fractions.tiff").touch()
     new_series = context.post_transfer(
-        tmp_path / "Position_1_[60.0]_fractions.tiff",
+        tmp_path / "Position_1_003_[60.0]_data_time_fractions.tiff",
         role="detector",
         required_position_files=[],
         required_strings=["fractions"],
@@ -233,6 +242,8 @@ def test_tomography_context_initialisation_for_serialem(tmp_path):
 def test_setting_tilt_series_size_and_completion_from_mdoc_parsing(
     mock_post, mock_get, tmp_path
 ):
+    mock_post.post().status_code = 200
+
     env = MurfeyInstanceEnvironment(
         url=urlparse("http://localhost:8000"),
         client_id=0,
@@ -251,21 +262,21 @@ def test_setting_tilt_series_size_and_completion_from_mdoc_parsing(
     assert context._tilt_series_sizes == {"test_1": 11}
     (tmp_path / "test_1.mdoc").touch()
     tilt = -50
-    (tmp_path / f"test_1_[{tilt:.1f}]_fractions.tiff").touch()
+    (tmp_path / f"test_1_001_[{tilt:.1f}]_data_time_fractions.tiff").touch()
     context.post_transfer(
-        tmp_path / f"test_1_[{tilt:.1f}]_fractions.tiff",
+        tmp_path / f"test_1_001_[{tilt:.1f}]_data_time_fractions.tiff",
         role="detector",
         environment=env,
         required_strings=["fractions"],
     )
     assert context._tilt_series == {
-        "test_1": [tmp_path / f"test_1_[{tilt:.1f}]_fractions.tiff"]
+        "test_1": [tmp_path / f"test_1_001_[{tilt:.1f}]_data_time_fractions.tiff"]
     }
-    for t in range(-40, 60, 10):
+    for i, t in enumerate(range(-40, 60, 10)):
         assert not context._completed_tilt_series
-        (tmp_path / f"test_1_[{t:.1f}]_fractions.tiff").touch()
+        (tmp_path / f"test_1_{i:03}_[{t:.1f}]_data_time_fractions.tiff").touch()
         context.post_transfer(
-            tmp_path / f"test_1_[{t:.1f}]_fractions.tiff",
+            tmp_path / f"test_1_{i:03}_[{t:.1f}]_data_time_fractions.tiff",
             role="detector",
             environment=env,
             required_strings=["fractions"],