Merge branch 'main' into ED-1-formats

src/dxtbx/boost_python/ext.cpp

@@ -195,35 +195,39 @@ namespace dxtbx { namespace boost_python {
     return PyBytes_FromStringAndSize(&*packed.begin(), packed.size());
   }
 
-  double distance_between_points(scitbx::vec2<int> const& a, scitbx::vec2<int> const& b) {
-    return std::sqrt((std::pow(double(b[0]-a[0]),2)+std::pow(double(b[1]-a[1]),2)));
+  double distance_between_points(scitbx::vec2<int> const &a,
+                                 scitbx::vec2<int> const &b) {
+    return std::sqrt(
+      (std::pow(double(b[0] - a[0]), 2) + std::pow(double(b[1] - a[1]), 2)));
   }
 
-  void radial_average(scitbx::af::versa<double, scitbx::af::flex_grid<> > & data,
-  scitbx::af::versa<bool, scitbx::af::flex_grid<> > & mask,
-  scitbx::vec2<int> const& beam_center,
-  scitbx::af::shared<double> sums,
-  scitbx::af::shared<double> sums_sq,
-  scitbx::af::shared<int> counts,
-  double pixel_size, double distance,
-  scitbx::vec2<int> const& upper_left,
-  scitbx::vec2<int> const& lower_right) {
+  void radial_average(scitbx::af::versa<double, scitbx::af::flex_grid<> > &data,
+                      scitbx::af::versa<bool, scitbx::af::flex_grid<> > &mask,
+                      scitbx::vec2<int> const &beam_center,
+                      scitbx::af::shared<double> sums,
+                      scitbx::af::shared<double> sums_sq,
+                      scitbx::af::shared<int> counts,
+                      double pixel_size,
+                      double distance,
+                      scitbx::vec2<int> const &upper_left,
+                      scitbx::vec2<int> const &lower_right) {
     std::size_t extent = sums.size();
     double extent_in_mm = extent * pixel_size;
-    double extent_two_theta = std::atan(extent_in_mm/distance)*180/scitbx::constants::pi;
-
-    for(std::size_t y = upper_left[1]; y < lower_right[1]; y++) {
-      for(std::size_t x = upper_left[0]; x < lower_right[0]; x++) {
-        double val = data(x,y);
-        if(val > 0 && mask(x,y)) {
-          scitbx::vec2<int> point((int)x,(int)y);
-          double d_in_mm = distance_between_points(point,beam_center) * pixel_size;
-          double twotheta = std::atan(d_in_mm/distance)*180/scitbx::constants::pi;
-          std::size_t bin = (std::size_t)std::floor(twotheta*extent/extent_two_theta);
-          if (bin >= extent)
-            continue;
+    double extent_two_theta =
+      std::atan(extent_in_mm / distance) * 180 / scitbx::constants::pi;
+
+    for (std::size_t y = upper_left[1]; y < lower_right[1]; y++) {
+      for (std::size_t x = upper_left[0]; x < lower_right[0]; x++) {
+        double val = data(x, y);
+        if (val > 0 && mask(x, y)) {
+          scitbx::vec2<int> point((int)x, (int)y);
+          double d_in_mm = distance_between_points(point, beam_center) * pixel_size;
+          double twotheta = std::atan(d_in_mm / distance) * 180 / scitbx::constants::pi;
+          std::size_t bin =
+            (std::size_t)std::floor(twotheta * extent / extent_two_theta);
+          if (bin >= extent) continue;
           sums[bin] += val;
-          sums_sq[bin] += val*val;
+          sums_sq[bin] += val * val;
           counts[bin]++;
         }
       }
@@ -261,11 +265,17 @@ namespace dxtbx { namespace boost_python {
     def("is_big_endian", is_big_endian);
     def("uncompress", &uncompress, (arg_("packed"), arg_("slow"), arg_("fast")));
     def("compress", &compress);
-    def("radial_average", &radial_average,
-      (arg("data"), arg("beam_center"), arg("sums"), arg("sums_sq"), arg("counts"),
-       arg("pixel_size"), arg("distance"),
-       arg("upper_left"), arg("lower_right")))
-    ;
+    def("radial_average",
+        &radial_average,
+        (arg("data"),
+         arg("beam_center"),
+         arg("sums"),
+         arg("sums_sq"),
+         arg("counts"),
+         arg("pixel_size"),
+         arg("distance"),
+         arg("upper_left"),
+         arg("lower_right")));
     def("uncompress_rod_TY6",
         &uncompress_rod_TY6,
         (arg_("data"), arg_("offsets"), arg_("slow"), arg_("fast")));

src/dxtbx/command_line/detector_superpose.py

@@ -3,12 +3,13 @@
 import math
 import sys
 
+from serialtbx.detector import iterate_detector_at_level
+
 from libtbx.phil import parse
 from libtbx.test_utils import approx_equal
 from scitbx.array_family import flex
 from scitbx.math.superpose import least_squares_fit
 from scitbx.matrix import col
-from serialtbx.detector import iterate_detector_at_level
 
 import dials.util
 from dials.util.options import OptionParser

src/dxtbx/command_line/image2pickle.py

@@ -12,13 +12,13 @@
 import sys
 
 import numpy as np
+import serialtbx.detector.cspad
+import serialtbx.util
 
 import libtbx.option_parser
 from libtbx import easy_pickle
 from libtbx.utils import Usage
-import serialtbx.util
 from scitbx.array_family import flex
-import serialtbx.detector.cspad
 
 import dxtbx.util
 

src/dxtbx/command_line/radial_average.py

@@ -16,10 +16,10 @@
 from libtbx.utils import Sorry, Usage
 from scitbx.array_family import flex
 from scitbx.matrix import col
-from dxtbx.ext import radial_average
 
 import dxtbx
 import dxtbx.util
+from dxtbx.ext import radial_average
 from dxtbx.model.experiment_list import ExperimentListFactory
 
 master_phil = iotbx.phil.parse(

src/dxtbx/format/FormatCBFMultiTile.py

@@ -8,8 +8,8 @@
 import numpy
 import pycbf
 
-from scitbx.array_family import flex
 from scitbx import matrix
+from scitbx.array_family import flex
 
 from dxtbx.format.FormatCBF import FormatCBF
 from dxtbx.format.FormatCBFFull import FormatCBFFull

src/dxtbx/format/FormatNexusJungfrauExt.py

@@ -4,11 +4,9 @@
 
 import h5py
 import numpy as np
-
-from scitbx.array_family import flex
-
 from serialtbx.detector.jungfrau import pad_stacked_format
 
+from scitbx.array_family import flex
 
 from dxtbx.format.FormatNexus import FormatNexus
 from dxtbx.format.nexus import h5str

src/dxtbx/format/FormatPYmultitile.py

@@ -5,11 +5,11 @@
 from calendar import timegm
 from time import strptime
 
+from serialtbx.detector.legacy_metrology.cspad_detector import CSPadDetector
+
 from iotbx.detectors.npy import image_dict_to_unicode
 from scitbx.matrix import col
 
-from serialtbx.detector.legacy_metrology.cspad_detector import CSPadDetector
-
 from dxtbx.format.FormatPY import FormatPY
 from dxtbx.model import Detector
 

src/dxtbx/format/FormatXTC.py

@@ -5,6 +5,8 @@
 import time
 
 import numpy as np
+import serialtbx.detector.xtc
+import serialtbx.util
 
 from libtbx.phil import parse
 from scitbx.array_family import flex
@@ -15,8 +17,6 @@
 from dxtbx.format.FormatStill import FormatStill
 from dxtbx.model import Spectrum
 from dxtbx.util.rotate_and_average import rotate_and_average
-import serialtbx.util
-import serialtbx.detector.xtc
 
 try:
     import psana

src/dxtbx/format/FormatXTCCspad.py

@@ -3,14 +3,14 @@
 import sys
 
 import numpy as np
+import serialtbx.detector.cspad
+from serialtbx.detector import cspad
+from serialtbx.detector.xtc import env_distance
 
 from cctbx.eltbx import attenuation_coefficient
 from libtbx.phil import parse
 from scitbx.array_family import flex
 from scitbx.matrix import col
-from serialtbx.detector import cspad
-from serialtbx.detector.xtc import env_distance
-import serialtbx.detector.cspad
 
 from dxtbx.format.FormatXTC import FormatXTC, locator_str
 from dxtbx.model import Detector, ParallaxCorrectedPxMmStrategy

src/dxtbx/format/FormatXTCEpix.py

@@ -62,7 +62,6 @@ def get_detector(self, index=None):
 
     def _detector(self, index=None):
         from PSCalib.SegGeometryStore import sgs
-
         from serialtbx.detector.xtc import basis_from_geo
 
         run = self.get_run_from_index(index)

src/dxtbx/format/FormatXTCJungfrau.py

@@ -103,7 +103,6 @@ def get_detector(self, index=None):
 
     def _detector(self, index=None):
         from PSCalib.SegGeometryStore import sgs
-
         from serialtbx.detector.xtc import basis_from_geo
 
         run = self.get_run_from_index(index)

src/dxtbx/format/FormatXTCRayonix.py

@@ -15,13 +15,13 @@
         raise
     psana = None
 
+from serialtbx.detector import rayonix
+
 from libtbx.phil import parse
 from scitbx.array_family import flex
 
 from dxtbx.format.FormatXTC import FormatXTC, locator_str
 
-from serialtbx.detector import rayonix
-
 rayonix_locator_str = """
   rayonix {
     bin_size = None

src/dxtbx/format/cbf_writer.py

@@ -13,12 +13,12 @@
 import sys
 
 import pycbf
+from serialtbx.detector import basis
 
-from dxtbx.format.FormatCBFMultiTile import cbf_wrapper
 from scitbx.array_family import flex
-from serialtbx.detector import basis
 
 import dxtbx.format.Registry
+from dxtbx.format.FormatCBFMultiTile import cbf_wrapper
 
 
 def add_frame_specific_cbf_tables(

src/dxtbx/format/nxmx_writer.py

@@ -14,14 +14,14 @@
 
 import h5py
 import numpy as np
+from serialtbx.detector import basis
 
 from cctbx import factor_ev_angstrom
 from libtbx import easy_pickle
 from libtbx.phil import parse
 from libtbx.utils import Sorry
 from scitbx import matrix
 from scitbx.array_family import flex
-from serialtbx.detector import basis
 
 from dials.util.options import ArgumentParser, flatten_experiments