fix wrong ordering of tilts and mishandling of extra tilts in mdoc

src/waretomo/_fix_mdoc.py

@@ -20,14 +20,21 @@ def _tilt_mdoc(
     if not dry_run:
         mdoc = Mdoc.from_file(mdoc_file)
         new_angles = iter(pd.read_csv(tlt_file, header=None)[0])
-        for i, section in enumerate(mdoc.section_data):
-            if i in skipped_tilts:
+        # mdoc is still out of order, but aretomo puts the new_angles in order
+        # this gives us tuples like (original_index, section), but ordered by angle
+        # like aretomo so we can compare it with the new angles
+        sorted_section_data = sorted(
+            enumerate(mdoc.section_data), key=lambda x: x[1].TiltAngle
+        )
+        for idx, section in sorted_section_data:
+            if idx in skipped_tilts:
                 continue
             try:
                 section.TiltAngle = next(new_angles)
             except StopIteration as e:
                 raise RuntimeError(
-                    f"not enough tilts generated by aretomo in {tlt_file}"
+                    f"not enough tilts generated by aretomo in {tlt_file}, "
+                    f"or Mdoc is corrupted"
                 ) from e
 
         try:

src/waretomo/_parse.py

@@ -2,6 +2,7 @@
 from xml.etree import ElementTree
 
 import mdocfile
+from rich import print
 
 
 def parse_data(
@@ -51,6 +52,18 @@ def parse_data(
         even = []
         valid_xml = None
         for i, tilt in enumerate(tilts):
+            if not tilt.exists():
+                print(
+                    f"[red]WARN: {tilt.name} is listed in an mdoc file, "
+                    "but the file does not exists."
+                )
+                print(
+                    "[red]      The tilt will be skipped, "
+                    "but you may want to check your data."
+                )
+                skipped_tilts.append(i)
+                continue
+
             xml = ElementTree.parse(tilt.with_suffix(".xml")).getroot()
             if xml.attrib["UnselectManual"] == "True":
                 skipped_tilts.append(i)

src/waretomo/main.py

@@ -207,7 +207,7 @@ def cli(
     if roi_dir is not None:
         roi_dir = Path(roi_dir)
 
-        pretrained_models = ("unet-3d-10a", "unet-3d-20a")
+    pretrained_models = ("unet-3d-10a", "unet-3d-20a")
     if train:
         if topaz_model in pretrained_models:
             raise click.UsageError(