Minor speed improvements for node creator

src/relion/zocalo/node_creator.py

@@ -272,7 +272,8 @@ def dummy(self, *args, **kwargs):
  with open(job_dir / "run.out", "w") as f:
  f.write(job_info.stdout)
  with open(job_dir / "run.err", "a") as f:
- f.write(f"{job_info.stderr}\n")
+ if job_info.stderr:
+ f.write(f"{job_info.stderr}\n")
  with open(job_dir / "note.txt", "a") as f:
  f.write(f"{job_info.command}\n")
 

src/relion/zocalo/spa_output_files.py

@@ -74,6 +74,7 @@ def _import_output_files(
 ):
  """Import jobs save a list of all micrographs"""
  star_file = job_dir / "movies.star"
+ added_line = [str(output_file), "1"]
 
  # Read and append to the existing output file, or otherwise create one
  if not star_file.exists():
@@ -83,13 +84,11 @@ def _import_output_files(
  movies_loop = data_movies.init_loop(
  "_rln", ["MicrographMovieName", "OpticsGroup"]
  )
+ movies_loop.add_row(added_line)
+ output_cif.write_file(str(star_file), style=cif.Style.Simple)
  else:
- output_cif = cif.read_file(str(star_file))
- data_movies = output_cif.find_block("movies")
- movies_loop = data_movies.find_loop("_rlnMicrographMovieName").get_loop()
-
- movies_loop.add_row([str(output_file), "1"])
- output_cif.write_file(str(star_file), style=cif.Style.Simple)
+ with open(star_file, "a") as output_cif:
+ output_cif.write(" ".join(added_line) + "\n")
 
 
 def _motioncorr_output_files(
@@ -101,6 +100,14 @@ def _motioncorr_output_files(
 ):
  """Motion correction saves a list of micrographs and their motion"""
  star_file = job_dir / "corrected_micrographs.star"
+ added_line = [
+ str(output_file),
+ str(output_file.with_suffix(".star")),
+ "1",
+ str(results["total_motion"]),
+ str(results["early_motion"]),
+ str(results["late_motion"]),
+ ]
 
  # Read and append to the existing output file, or otherwise create one
  if not star_file.exists():
@@ -118,22 +125,11 @@ def _motioncorr_output_files(
  "AccumMotionLate",
  ],
  )
+ movies_loop.add_row(added_line)
+ output_cif.write_file(str(star_file), style=cif.Style.Simple)
  else:
- output_cif = cif.read_file(str(star_file))
- data_movies = output_cif.find_block("micrographs")
- movies_loop = data_movies.find_loop("_rlnMicrographName").get_loop()
-
- movies_loop.add_row(
- [
- str(output_file),
- str(output_file.with_suffix(".star")),
- "1",
- str(results["total_motion"]),
- str(results["early_motion"]),
- str(results["late_motion"]),
- ]
- )
- output_cif.write_file(str(star_file), style=cif.Style.Simple)
+ with open(star_file, "a") as output_cif:
+ output_cif.write(" ".join(added_line) + "\n")
 
  # Logfile is expected but will not be made
  (star_file.parent / "logfile.pdf").touch()
@@ -149,6 +145,21 @@ def _ctffind_output_files(
  """Ctf estimation saves a list of micrographs and their ctf parameters"""
  star_file = job_dir / "micrographs_ctf.star"
 
+ # Results needed in the star file are stored in a txt file with the output
+ with open(output_file.with_suffix(".txt"), "r") as f:
+ ctf_results = f.readlines()[-1].split()
+ added_line = [
+ str(input_file),
+ "1",
+ str(output_file.with_suffix(".ctf")) + ":mrc",
+ ctf_results[1],
+ ctf_results[2],
+ str(abs(float(ctf_results[1]) - float(ctf_results[2]))),
+ ctf_results[3],
+ ctf_results[5],
+ ctf_results[6],
+ ]
+
  # Read and append to the existing output file, or otherwise create one
  if not star_file.exists():
  output_cif = get_optics_table(relion_options)
@@ -168,29 +179,11 @@ def _ctffind_output_files(
  "CtfMaxResolution",
  ],
  )
+ movies_loop.add_row(added_line)
+ output_cif.write_file(str(star_file), style=cif.Style.Simple)
  else:
- output_cif = cif.read_file(str(star_file))
- data_movies = output_cif.find_block("micrographs")
- movies_loop = data_movies.find_loop("_rlnMicrographName").get_loop()
-
- # Results needed in the star file are stored in a txt file with the output
- with open(output_file.with_suffix(".txt"), "r") as f:
- ctf_results = f.readlines()[-1].split()
-
- movies_loop.add_row(
- [
- str(input_file),
- "1",
- str(output_file.with_suffix(".ctf")) + ":mrc",
- ctf_results[1],
- ctf_results[2],
- str(abs(float(ctf_results[1]) - float(ctf_results[2]))),
- ctf_results[3],
- ctf_results[5],
- ctf_results[6],
- ]
- )
- output_cif.write_file(str(star_file), style=cif.Style.Simple)
+ with open(star_file, "a") as output_cif:
+ output_cif.write(" ".join(added_line) + "\n")
 
  # Logfile is expected but will not be made
  (star_file.parent / "logfile.pdf").touch()
@@ -242,6 +235,14 @@ def _icebreaker_output_files(
  return
 
  # Read and append to the existing output file, or otherwise create one
+ added_line = [
+ file_to_add,
+ str(input_file.with_suffix(".star")),
+ "1",
+ str(results["total_motion"]),
+ str(results["early_motion"]),
+ str(results["late_motion"]),
+ ]
  if not star_file.exists():
  output_cif = cif.Document()
 
@@ -257,22 +258,11 @@ def _icebreaker_output_files(
  "AccumMotionLate",
  ],
  )
+ movies_loop.add_row(added_line)
+ output_cif.write_file(str(star_file), style=cif.Style.Simple)
  else:
- output_cif = cif.read_file(str(star_file))
- data_movies = output_cif.find_block("micrographs")
- movies_loop = data_movies.find_loop("_rlnMicrographName").get_loop()
-
- movies_loop.add_row(
- [
- file_to_add,
- str(input_file.with_suffix(".star")),
- "1",
- str(results["total_motion"]),
- str(results["early_motion"]),
- str(results["late_motion"]),
- ]
- )
- output_cif.write_file(str(star_file), style=cif.Style.Simple)
+ with open(star_file, "a") as output_cif:
+ output_cif.write(" ".join(added_line) + "\n")
 
 
 def _cryolo_output_files(
@@ -284,6 +274,7 @@ def _cryolo_output_files(
 ):
  """Cryolo jobs save a list of micrographs and files with particle coordinates"""
  star_file = job_dir / "autopick.star"
+ added_line = [str(input_file), str(output_file)]
 
  # Read and append to the existing output file, or otherwise create one
  if not star_file.exists():
@@ -297,13 +288,11 @@ def _cryolo_output_files(
  "MicrographCoordinates",
  ],
  )
+ movies_loop.add_row(added_line)
+ output_cif.write_file(str(star_file), style=cif.Style.Simple)
  else:
- output_cif = cif.read_file(str(star_file))
- data_movies = output_cif.find_block("coordinate_files")
- movies_loop = data_movies.find_loop("_rlnMicrographName").get_loop()
-
- movies_loop.add_row([str(input_file), str(output_file)])
- output_cif.write_file(str(star_file), style=cif.Style.Simple)
+ with open(star_file, "a") as output_cif:
+ output_cif.write(" ".join(added_line) + "\n")
 
 
 def _extract_output_files(