Merge pull request #59 from scipion-em/devel

fix aln parsing again :)

CHANGES.txt

@@ -1,3 +1,4 @@
+3.8.1: bugfix for reading aln file with dark views removed
 3.8:
     - add aretomo2 1.0.0
     - fix output aln file parsing during local alignment

aretomo/__init__.py

@@ -32,7 +32,7 @@
 from .constants import *
 
 
-__version__ = '3.8'
+__version__ = '3.8.1'
 _logo = "aretomo_logo.png"
 _references = ['Zheng2022']
 

aretomo/convert.py

@@ -63,11 +63,24 @@ def readAlnFile(alignFn: Union[str, os.PathLike]) -> Type[AretomoAln]:
     aln2xf conversion taken from https://github.com/brisvag/stemia/blob/main/stemia/aretomo/aln2xf.py
     """
     # Read number of sections, as we need to ignore local alignments part of the file
+    comments = []
     with open(alignFn) as f:
-        f.readline()
-        numSec = f.readline().strip("#").split()[-1]
+        for line in f:
+            if line.startswith("# SEC"):
+                break
+            else:
+                comments.append(line)
 
-    data = np.loadtxt(alignFn, dtype=float, comments='#', skiprows=4, max_rows=int(numSec))
+    numSec, darkNum = 0, 0
+    for c in comments:
+        if c.startswith("# RawSize"):
+            numSec = int(c.split()[-1])
+        elif c.startswith("# DarkFrame"):
+            darkNum += 1
+
+    data = np.loadtxt(alignFn, dtype=float, comments='#',
+                      skiprows=len(comments)+1,
+                      max_rows=numSec-darkNum)
     AretomoAln.sections = list(data[:, 0].astype(int))  # SEC
     AretomoAln.tilt_angles = data[:, -1]  # TILT
     AretomoAln.tilt_axes = data[:, 1]  # ROT