Remove calls to get tilt series and tag (#376)

Author: stephen-riggs

src/murfey/client/contexts/tomo.py

@@ -4,7 +4,7 @@
 from datetime import datetime
 from pathlib import Path
 from threading import RLock
-from typing import Callable, Dict, List, NamedTuple, Optional, OrderedDict
+from typing import Callable, Dict, List, Optional, OrderedDict
 
 import requests
 import xmltodict
@@ -27,95 +27,34 @@
 requests.get, requests.post, requests.put, requests.delete = authorised_requests()
 
 
-class TiltInfoExtraction(NamedTuple):
-    series: Callable[[Path], str]
-    angle: Callable[[Path], str]
-    tag: Callable[[Path], str]
-
-
-def _get_tilt_series_v5_7(p: Path) -> str:
-    return p.name.split("_")[1]
-
-
 def _get_tilt_angle_v5_7(p: Path) -> str:
     return p.name.split("[")[1].split("]")[0]
 
 
-def _get_tilt_tag_v5_7(p: Path) -> str:
-    return p.name.split("_")[0]
-
-
-def _get_slice_index_v5_11(tag: str) -> int:
-    slice_index = 0
-    for i, ch in enumerate(tag[::-1]):
-        if not ch.isnumeric():
-            slice_index = -i
-            break
-    if not slice_index:
-        raise ValueError(
-            f"The file tag {tag} does not end in numeric characters or is entirely numeric: cannot parse"
-        )
-    return slice_index
-
-
-def _get_tilt_series_v5_11(p: Path) -> str:
-    tag = p.name.split("_")[0]
-    slice_index = _get_slice_index_v5_11(tag)
-    return tag[slice_index:]
-
-
-def _get_tilt_tag_v5_11(p: Path) -> str:
-    tag = p.name.split("_")[0]
-    slice_index = _get_slice_index_v5_11(tag)
-    return tag[:slice_index]
-
-
 def _get_tilt_angle_v5_11(p: Path) -> str:
     _split = p.name.split("_")[2].split(".")
     return ".".join(_split[:-1])
 
 
 def _find_angle_index(split_name: List[str]) -> int:
     for i, part in enumerate(split_name):
-        if "." in part:
+        if "." in part and part[0].isnumeric():
             return i
-    return 0
-
-
-def _get_tilt_series_v5_12(p: Path) -> str:
-    split_name = p.name.split("_")
-    angle_idx = _find_angle_index(split_name)
-    if split_name[angle_idx - 2].isnumeric():
-        return split_name[angle_idx - 2]
-    return ""
+    return -1
 
 
 def _get_tilt_angle_v5_12(p: Path) -> str:
-    split_name = p.name.split("_")
+    split_name = p.stem.split("_")
     angle_idx = _find_angle_index(split_name)
+    if angle_idx == -1:
+        return ""
     return split_name[angle_idx]
 
 
-def _get_tilt_tag_v5_12(p: Path) -> str:
-    split_name = p.name.split("_")
-    angle_idx = _find_angle_index(split_name)
-    if split_name[angle_idx - 2].isnumeric():
-        return "_".join(split_name[: angle_idx - 2])
-    return "_".join(split_name[: angle_idx - 1])
-
-
 tomo_tilt_info = {
-    "5.7": TiltInfoExtraction(
-        _get_tilt_series_v5_7, _get_tilt_angle_v5_7, _get_tilt_tag_v5_7
-    ),
-    "5.11": TiltInfoExtraction(
-        _get_tilt_series_v5_11, _get_tilt_angle_v5_11, _get_tilt_tag_v5_11
-    ),
-    "5.12": TiltInfoExtraction(
-        _get_tilt_series_v5_12,
-        _get_tilt_angle_v5_12,
-        _get_tilt_tag_v5_12,
-    ),
+    "5.7": _get_tilt_angle_v5_7,
+    "5.11": _get_tilt_angle_v5_11,
+    "5.12": _get_tilt_angle_v5_12,
 }
 
 
@@ -177,8 +116,6 @@ def __init__(self, acquisition_software: str, basepath: Path):
         self._processing_job_stash: dict = {}
         self._preprocessing_triggers: dict = {}
         self._lock: RLock = RLock()
-        self._extract_tilt_series: Callable[[Path], str] | None = None
-        self._extract_tilt_tag: Callable[[Path], str] | None = None
 
     def _flush_data_collections(self):
         logger.info(
@@ -232,14 +169,7 @@ def _check_for_alignment(
         manual_tilt_offset: Optional[float],
         pixel_size: Optional[float],
     ):
-        if self._extract_tilt_series and self._extract_tilt_tag:
-            tilt_series = (
-                f"{self._extract_tilt_tag(movie_path)}_{self._extract_tilt_series(movie_path)}"
-                if self._extract_tilt_tag(movie_path)
-                else self._extract_tilt_series(movie_path)
-            )
-        else:
-            return
+        tilt_series = _construct_tilt_series_name(movie_path)
 
         if self._motion_corrected_tilt_series.get(
             tilt_series
@@ -370,9 +300,7 @@ def _get_source(
     def _add_tilt(
         self,
         file_path: Path,
-        extract_tilt_series: Callable[[Path], str],
         extract_tilt_angle: Callable[[Path], str],
-        extract_tilt_tag: Callable[[Path], str],
         environment: MurfeyInstanceEnvironment | None = None,
         required_position_files: List[Path] | None = None,
         required_strings: List[str] | None = None,
@@ -390,10 +318,6 @@ def _add_tilt(
         )
         if required_strings and not any(r in file_path.name for r in required_strings):
             return []
-        if not self._extract_tilt_series:
-            self._extract_tilt_series = extract_tilt_series
-        if not self._extract_tilt_tag:
-            self._extract_tilt_tag = extract_tilt_tag
         try:
             tilt_angle = extract_tilt_angle(file_path)
             try:
@@ -733,9 +657,7 @@ def _add_tomo_tilt(
         tilt_series = _construct_tilt_series_name(file_path)
         return self._add_tilt(
             file_path,
-            tilt_info_extraction.series,
-            tilt_info_extraction.angle,
-            tilt_info_extraction.tag,
+            tilt_info_extraction,
             environment=environment,
             required_position_files=(
                 required_position_files
@@ -767,9 +689,7 @@ def _extract_tilt_series(p: Path) -> str:
 
         return self._add_tilt(
             file_path,
-            _extract_tilt_series,
             lambda x: ".".join(x.name.split(delimiter)[-1].split(".")[:-1]),
-            lambda x: "",
             environment=environment,
             required_strings=[],
         )