Change logger statements in spot finding to use f-strings to ensure l…

…ogger info is always printed correctly.

newsfragments/XXX.bugfix

@@ -0,0 +1 @@
+Change logger statements in spot finding to use f-strings to ensure logger info is always printed correctly.

src/dials/algorithms/spot_finding/factory.py

@@ -242,7 +242,7 @@ def __call__(self, flags, **kwargs):
  flags = self.run(flags, **kwargs)
  num_after = flags.count(True)
  logger.info(
- "Filtered %d of %d spots by peak-centroid distance", num_after, num_before
+ f"Filtered {num_after} of {num_before} spots by peak-centroid distance"
  )
  return flags
 
@@ -332,7 +332,7 @@ def __call__(self, flags, **kwargs):
  flags = self.run(flags, **kwargs)
  num_after = flags.count(True)
  logger.info(
- "Filtered %d of %d spots by background gradient", num_after, num_before
+ f"Filtered {num_after} of {num_before} spots by background gradient"
  )
  return flags
 
@@ -380,7 +380,7 @@ def run(self, flags, sequence=None, observations=None, **kwargs): # noqa: U100
  cutoff = hist.slot_centers()[i - 1] - 0.5 * hist.slot_width()
 
  sel = np.column_stack(np.where(H > cutoff))
- for (ix, iy) in sel:
+ for ix, iy in sel:
  flags.set_selected(
  (
  (obs_x > xedges[ix])
@@ -398,7 +398,7 @@ def __call__(self, flags, **kwargs):
  num_before = flags.count(True)
  flags = self.run(flags, **kwargs)
  num_after = flags.count(True)
- logger.info("Filtered %d of %d spots by spot density", num_after, num_before)
+ logger.info(f"Filtered {num_after} of {num_before} spots by spot density")
  return flags
 
 

src/dials/algorithms/spot_finding/finder.py

@@ -86,9 +86,7 @@ def __call__(self, index):
  mask = tuple(m1 & m2 for m1, m2 in zip(mask, self.mask))
 
  logger.debug(
- "Number of masked pixels for image %i: %i",
- index,
- sum(m.count(False) for m in mask),
+ f"Number of masked pixels for image {index}: {sum(m.count(False) for m in mask)}",
  )
 
  # Add the images to the pixel lists
@@ -154,13 +152,10 @@ def __call__(self, index):
  # Print some info
  if self.compute_mean_background:
  logger.info(
- "Found %d strong pixels on image %d with average background %f",
- num_strong,
- frame + 1,
- average_background,
+ f"Found {num_strong} strong pixels on image {frame + 1} with average background {average_background}",
  )
  else:
- logger.info("Found %d strong pixels on image %d", num_strong, frame + 1)
+ logger.info(f"Found {num_strong} strong pixels on image {frame + 1}")
 
  # Return the result
  return pixel_list
@@ -295,16 +290,16 @@ def pixel_list_to_shoeboxes(
  shoeboxes.extend(creator.result())
  spotsizes.extend(creator.spot_size())
  hp.extend(creator.hot_pixels())
- logger.info("\nExtracted %d spots", len(shoeboxes))
+ logger.info(f"\nExtracted {len(shoeboxes)} spots")
 
  # Get the unallocated spots and print some info
  selection = shoeboxes.is_allocated()
  shoeboxes = shoeboxes.select(selection)
  ntoosmall = (spotsizes < min_spot_size).count(True)
  ntoolarge = (spotsizes > max_spot_size).count(True)
  assert ntoosmall + ntoolarge == selection.count(False)
- logger.info("Removed %d spots with size < %d pixels", ntoosmall, min_spot_size)
- logger.info("Removed %d spots with size > %d pixels", ntoolarge, max_spot_size)
+ logger.info(f"Removed {ntoosmall} spots with size < {min_spot_size} pixels")
+ logger.info(f"Removed {ntoolarge} spots with size > {max_spot_size} pixels")
 
  # Return the shoeboxes
  return shoeboxes, hotpixels
@@ -316,11 +311,11 @@ def shoeboxes_to_reflection_table(
  """Filter shoeboxes and create reflection table"""
  # Calculate the spot centroids
  centroid = shoeboxes.centroid_valid()
- logger.info("Calculated %d spot centroids", len(shoeboxes))
+ logger.info(f"Calculated {len(shoeboxes)} spot centroids")
 
  # Calculate the spot intensities
  intensity = shoeboxes.summed_intensity()
- logger.info("Calculated %d spot intensities", len(shoeboxes))
+ logger.info(f"Calculated {len(shoeboxes)} spot intensities")
 
  # Create the observations
  observed = flex.observation(shoeboxes.panels(), centroid, intensity)
@@ -459,7 +454,7 @@ def _find_spots(self, imageset):
  mp_chunksize = self._compute_chunksize(
  len(imageset), mp_njobs * mp_nproc, self.min_chunksize
  )
- logger.info("Setting chunksize=%i", mp_chunksize)
+ logger.info(f"Setting chunksize={mp_chunksize}")
 
  len_by_nproc = int(math.floor(len(imageset) / (mp_njobs * mp_nproc)))
  if mp_chunksize > len_by_nproc:
@@ -492,13 +487,10 @@ def _find_spots(self, imageset):
  logger.info("Extracting strong pixels from images")
  if mp_njobs > 1:
  logger.info(
- " Using %s with %d parallel job(s) and %d processes per node\n",
- mp_method,
- mp_njobs,
- mp_nproc,
+ f" Using {mp_method} with {mp_njobs} parallel job(s) and {mp_nproc} processes per node\n"
  )
  else:
- logger.info(" Using multiprocessing with %d parallel job(s)\n", mp_nproc)
+ logger.info(f" Using multiprocessing with {mp_nproc} parallel job(s)\n")
  if mp_nproc > 1 or mp_njobs > 1:
 
  def process_output(result):
@@ -555,7 +547,7 @@ def _find_spots_2d_no_shoeboxes(self, imageset):
  mp_chunksize = self._compute_chunksize(
  len(imageset), mp_njobs * mp_nproc, self.min_chunksize
  )
- logger.info("Setting chunksize=%i", mp_chunksize)
+ logger.info(f"Setting chunksize={mp_chunksize}")
 
  len_by_nproc = int(math.floor(len(imageset) / (mp_njobs * mp_nproc)))
  if mp_chunksize > len_by_nproc:
@@ -588,13 +580,10 @@ def _find_spots_2d_no_shoeboxes(self, imageset):
  logger.info("Extracting strong spots from images")
  if mp_njobs > 1:
  logger.info(
- " Using %s with %d parallel job(s) and %d processes per node\n",
- mp_method,
- mp_njobs,
- mp_nproc,
+ f" Using {mp_method} with {mp_njobs} parallel job(s) and {mp_nproc} processes per node\n"
  )
  else:
- logger.info(" Using multiprocessing with %d parallel job(s)\n", mp_nproc)
+ logger.info(f" Using multiprocessing with {mp_nproc} parallel job(s)\n")
  if mp_nproc > 1 or mp_njobs > 1:
 
  def process_output(result):
@@ -701,7 +690,7 @@ def find_spots(self, experiments: ExperimentList) -> flex.reflection_table:
 
  # Find the strong spots in the sequence
  logger.info(
- "-" * 80 + "\nFinding strong spots in imageset %d\n" + "-" * 80, j
+ "-" * 80 + f"\nFinding strong spots in imageset {j}\n" + "-" * 80
  )
  table, hot_mask = self._find_spots_in_imageset(imageset)
 
@@ -811,7 +800,7 @@ def _find_spots_in_imageset(self, imageset):
  )
  )
 
- logger.info("\nFinding spots in image %s to %s...", j0, j1)
+ logger.info(f"\nFinding spots in image {j0} to {j1}...")
  j0 -= 1
  if isinstance(imageset, ImageSequence):
  j0 -= imageset.get_array_range()[0]
@@ -849,7 +838,7 @@ def _create_hot_mask(self, imageset, hot_pixels):
  for i in range(len(hp)):
  hm[hp[i]] = False
  num_hot += len(hp)
- logger.info("Found %d possible hot pixel(s)", num_hot)
+ logger.info(f"Found {num_hot} possible hot pixel(s)")
 
  else:
  hot_mask = None
@@ -913,7 +902,6 @@ def __init__(
  self.experiments = experiments
 
  def _correct_centroid_tof(self, reflections):
-
  """
  Sets the centroid of the spot to the peak position along the
  time of flight, as this tends to more accurately represent the true