Fix compatibility with latest AreTomo version 1.1.2

Author: abartesaghi

src/pyp/align/core.py

@@ -5194,7 +5194,7 @@ def align_tilt_series(name, parameters, rotation=0):
 -AlignZ {specimen_thickness} \
 {reconstruct_option} \
 -TiltCor {tilt_offset_option} \
--OutImod 1 {patches} \
+-OutImod 2 {patches} \
 -Gpu {get_gpu_id()}"
             [ output, error ] = run_shell_command(command, verbose=parameters["slurm_verbose"])
 

src/pyp/merge/core.py

@@ -12,6 +12,7 @@
 from pyp import utils
 from pyp.analysis import plot
 from pyp.inout.image import mrc
+from pyp.inout.image.core import get_image_dimensions
 from pyp.inout.utils import pyp_edit_box_files as imod
 from pyp.merge import weights as pyp_weights
 from pyp.system import project_params
@@ -315,10 +316,25 @@ def reconstruct_tomo(parameters, name, x, y, binning, zfact, tilt_options, force
             if not parameters["tomo_rec_aretomo_sart"]:
                 reconstruct_option = "-Wbp 1"
 
+            # the new version of AreTomo2 apparently need the alignments
+            if not os.path.exists(f"{name}.aln"):
+                tilt_angles = np.loadtxt(f"{name}.tlt",ndmin=2)
+                tilt_order = np.loadtxt(f"{name}.order",ndmin=2)
+                x, y, z = get_image_dimensions(f"{name}.ali")
+                with open(f"{name}.aln",'w') as f:
+                    f.write("# AreTomo Alignment / Priims bprmMn)\n")
+                    f.write(f"# RawSize = {x} {y} {z}\n")
+                    f.write(f"# NumPatches = 0\n")
+                    f.write(f"# SEC     ROT         GMAG       TX          TY      SMEAN     SFIT    SCALE     BASE     TILT\n")
+                    for tilt, order in zip(tilt_angles, tilt_order):
+                        #    0    00.0000    1.00000   1493.353   -740.186     1.00     1.00     1.00     0.00    -60.00
+                        f.write("%5d%11.4f%11.5f%11.3f%11.3f%9.2f%9.2f%9.2f%9.2f%9.2f\n" % (order,0,1,0,0,1,1,1,0,tilt))
+
             command = f"{get_aretomo_path()} \
 -InMrc {name}.ali \
 -OutMrc {name}.rec \
 -AngFile {name}.tlt \
+-AlnFile {name}.aln \
 -VolZ {int(1.0 * thickness)} \
 -OutBin {binning} \
 -DarkTol {parameters['tomo_ali_aretomo_dark_tol']} \

src/pyp/preprocess/core.py

@@ -312,7 +312,7 @@ def read_tilt_series(
                 try:
                     shutil.copy2(rawtlt, "{0}.rawtlt".format(name))
                 except:
-                    # ignore of file already exists
+                    # ignore if file already exists
                     pass
             elif os.path.isfile(filename + ".mrc.mdoc"):
                 local_run.run_shell_command(