DIALS 3.1.3

- ``dxtbx.image_average``: Better use of MPI to avoid errors and increase performance (cctbx#207)
- Update DLS I23 bad pixel mask after detector has been cleaned, fixing previously bad modules. (cctbx#220)
- Change default bit depth for DLS Eigers where header information is missing

CHANGELOG.rst

@@ -1,3 +1,16 @@
+DIALS 3.1.3 (2020-09-28)
+========================
+
+Bugfixes
+--------
+
+- ``dxtbx.image_average``: Better use of MPI to avoid errors and increase
+  performance (#207)
+- Update DLS I23 bad pixel mask after detector has been cleaned, fixing
+  previously bad modules. (#220)
+- Change default bit depth for DLS eigers where header information is missing
+
+
 DIALS 3.1.1 (2020-09-01)
 ========================
 

command_line/image_average.py

@@ -10,6 +10,7 @@
 import copy
 import sys
 from builtins import range
+import numpy as np
 
 import libtbx.load_env
 from libtbx import easy_mp, option_parser
@@ -284,7 +285,7 @@ def run(argv=None):
         iterable = iterable[command_line.options.skip_images :]
     if (
         command_line.options.num_images_max is not None
-        and command_line.options.num_images_max < iterable
+        and command_line.options.num_images_max < len(iterable)
     ):
         iterable = iterable[: command_line.options.num_images_max]
     assert len(iterable) >= 2, "Need more than one image to average"
@@ -308,14 +309,39 @@ def run(argv=None):
         # chop the list into pieces, depending on rank.  This assigns each process
         # events such that the get every Nth event where N is the number of processes
         iterable = [i for n, i in enumerate(iterable) if (n + rank) % size == 0]
-        results = [worker(iterable)]
-        results = comm.gather(results, root=0)
+        r_nfail, r_nmemb, r_max_img, r_sum_distance, r_sum_img, r_ssq_img, r_sum_wavelength = worker(
+            iterable
+        )
+
+        nfail = np.array([0])
+        nmemb = np.array([0])
+        sum_distance = np.array([0.0])
+        sum_wavelength = np.array([0.0])
+        comm.Reduce(np.array([r_nfail]), nfail)
+        comm.Reduce(np.array([r_nmemb]), nmemb)
+        comm.Reduce(np.array([r_sum_distance]), sum_distance)
+        comm.Reduce(np.array([r_sum_wavelength]), sum_wavelength)
+        nfail = int(nfail[0])
+        nmemb = int(nmemb)
+        sum_distance = float(sum_distance[0])
+        sum_wavelength = float(sum_wavelength[0])
+
+        def reduce_image(data, op=MPI.SUM):
+            result = []
+            for panel_data in data:
+                panel_data = panel_data.as_numpy_array()
+                reduced_data = np.zeros(panel_data.shape).astype(panel_data.dtype)
+                comm.Reduce(panel_data, reduced_data, op=op)
+                result.append(flex.double(reduced_data))
+            return result
+
+        max_img = reduce_image(r_max_img, MPI.MAX)
+        sum_img = reduce_image(r_sum_img)
+        ssq_img = reduce_image(r_ssq_img)
+
         if rank != 0:
             return
-        results_set = []
-        for r in results:
-            results_set.extend(r)
-        results = results_set
+        avg_img = tuple(s / nmemb for s in sum_img)
     else:
         if command_line.options.nproc == 1:
             results = [worker(iterable)]
@@ -325,38 +351,38 @@ def run(argv=None):
                 func=worker, iterable=iterable, processes=command_line.options.nproc
             )
 
-    nfail = 0
-    nmemb = 0
-    for (
-        i,
-        (
-            r_nfail,
-            r_nmemb,
-            r_max_img,
-            r_sum_distance,
-            r_sum_img,
-            r_ssq_img,
-            r_sum_wavelength,
-        ),
-    ) in enumerate(results):
-        nfail += r_nfail
-        nmemb += r_nmemb
-        if i == 0:
-            max_img = r_max_img
-            sum_distance = r_sum_distance
-            sum_img = r_sum_img
-            ssq_img = r_ssq_img
-            sum_wavelength = r_sum_wavelength
-        else:
-            for p in range(len(sum_img)):
-                sel = (r_max_img[p] > max_img[p]).as_1d()
-                max_img[p].set_selected(sel, r_max_img[p].select(sel))
+        nfail = 0
+        nmemb = 0
+        for (
+            i,
+            (
+                r_nfail,
+                r_nmemb,
+                r_max_img,
+                r_sum_distance,
+                r_sum_img,
+                r_ssq_img,
+                r_sum_wavelength,
+            ),
+        ) in enumerate(results):
+            nfail += r_nfail
+            nmemb += r_nmemb
+            if i == 0:
+                max_img = r_max_img
+                sum_distance = r_sum_distance
+                sum_img = r_sum_img
+                ssq_img = r_ssq_img
+                sum_wavelength = r_sum_wavelength
+            else:
+                for p in range(len(sum_img)):
+                    sel = (r_max_img[p] > max_img[p]).as_1d()
+                    max_img[p].set_selected(sel, r_max_img[p].select(sel))
 
-                sum_img[p] += r_sum_img[p]
-                ssq_img[p] += r_ssq_img[p]
+                    sum_img[p] += r_sum_img[p]
+                    ssq_img[p] += r_ssq_img[p]
 
-            sum_distance += r_sum_distance
-            sum_wavelength += r_sum_wavelength
+                sum_distance += r_sum_distance
+                sum_wavelength += r_sum_wavelength
 
     # Early exit if no statistics were accumulated.
     if command_line.options.verbose:

format/FormatCBFMiniPilatusDLS12M.py

@@ -170,7 +170,11 @@ def _mask_bad_modules(self, detector):
         cy = 97  # chip pixels y
         dx = 7  # module gap size
 
-        if timestamp > calendar.timegm((2020, 2, 21, 0, 0, 0)):
+        if timestamp > calendar.timegm((2020, 9, 8, 0, 0, 0)):
+            # 2020 run 4
+            # Detector serviced by Dectris, no bad modules
+            pass
+        elif timestamp > calendar.timegm((2020, 2, 21, 0, 0, 0)):
             # 2020 run 1
             # module @ row 1 column 4
             # blank chip @ row 15 column 4 (chip row 0, column 1)

format/FormatNexusEigerDLS.py

@@ -67,7 +67,7 @@ def __init__(self, image_file, **kwargs):
             self._meta = find_meta_filename(image_file)
             self._bit_depth_image = get_bit_depth_from_meta(self._meta)
         except Exception:
-            self._bit_depth_image = 0
+            self._bit_depth_image = 16
 
     def get_detector(self, index=None):
         # workaround for https://jira.diamond.ac.uk/browse/I03-365

tests/command_line/test_average.py

@@ -6,18 +6,29 @@
 
 import dxtbx
 
+import pytest
+
+
+@pytest.mark.parametrize("use_mpi", [True, False])
+def test_average(dials_regression, tmpdir, use_mpi):
+    # Only allow MPI tests if we've got MPI capabilities
+    if use_mpi:
+        pytest.importorskip("mpi4py")
 
-def test_average(dials_regression, tmpdir):
     data = os.path.join(
         dials_regression,
         "image_examples",
         "SACLA_MPCCD_Cheetah",
         "run266702-0-subset.h5",
     )
+    if use_mpi:
+        command = "mpirun"
+        mpargs = "-n 2 dxtbx.image_average".split()
+    else:
+        command = "dxtbx.image_average"
+        mpargs = "-n 2".split()
     result = procrunner.run(
-        ["dxtbx.image_average"]
-        + "-v -a avg.cbf -s stddev.cbf -m max.cbf".split()
-        + [data],
+        [command] + mpargs + "-v -a avg.cbf -s stddev.cbf -m max.cbf".split() + [data],
         working_directory=tmpdir,
     )
     assert not result.returncode and not result.stderr

tests/format/test_FormatCBFMiniPilatusDLS12M.py

@@ -33,6 +33,8 @@
             False,
             293699 + n_pixels_vertical_gaps,
         ),
+        (calendar.timegm((2020, 9, 8, 0, 0, 1)), True, 3053),
+        (calendar.timegm((2020, 9, 8, 0, 0, 1)), False, 3053 + n_pixels_vertical_gaps),
     ),
 )
 def test_bad_pixel_mask(