Additional methods for FormatISISSXD to extract data more efficiently. (

#743)

newsfragments/743.misc

@@ -0,0 +1 @@
+Additional methods for FormatISISSXD to extract data more efficiently.

src/dxtbx/format/FormatISISSXD.py

@@ -3,6 +3,7 @@
 from typing import List, Tuple
 
 import h5py
+import numpy as np
 
 import cctbx.array_family.flex as flex
 
@@ -44,6 +45,9 @@ def get_name(image_file: str) -> str:
 
  return get_name(image_file) == "SXD"
 
+ def get_instrument_name(self) -> str:
+ return "SXD"
+
  def get_experiment_title(self) -> str:
  return self._nxs_file["raw_data_1"]["title"][0].decode()
 
@@ -55,23 +59,26 @@ def get_experiment_description(self) -> str:
  run_number = self.get_experiment_run_number()
  return f"{title} ({run_number})"
 
- def get_goniometer(self, idx: int = None) -> Goniometer:
- rotation_axis = (0.0, 1.0, 0.0)
- fixed_rotation = (1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0)
- goniometer = GoniometerFactory.make_goniometer(rotation_axis, fixed_rotation)
+ def get_goniometer_phi_angle(self) -> float:
  try:
  experiment_title = self.get_experiment_title()
  if "w=" in experiment_title:
- angle = float(experiment_title().split("w=")[1].split()[0])
+ return float(experiment_title.split("w=")[1].split()[0])
  elif "wccr" in experiment_title:
- angle = float(experiment_title.split("wccr=")[1].split()[0])
+ return float(experiment_title.split("wccr=")[1].split()[0])
  elif "wtl" in experiment_title:
- angle = float(experiment_title.split("wtl=")[1].split()[0])
+ return float(experiment_title.split("wtl=")[1].split()[0])
  else:
- return goniometer
- goniometer.rotate_around_origin(rotation_axis, angle)
+ return 0
  except (ValueError, IndexError):
- pass
+ return 0
+
+ def get_goniometer(self, idx: int = None) -> Goniometer:
+ rotation_axis = (0.0, 1.0, 0.0)
+ fixed_rotation = (1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0)
+ goniometer = GoniometerFactory.make_goniometer(rotation_axis, fixed_rotation)
+ angle = self.get_goniometer_phi_angle()
+ goniometer.rotate_around_origin(rotation_axis, angle)
  return goniometer
 
  def get_detector(self, index: int = None) -> Detector:
@@ -313,3 +320,71 @@ def get_raw_data(self, index: int, use_loaded_data=True) -> Tuple[flex.int]:
  raw_data.append(panel_data)
 
  return tuple(raw_data)
+
+ def get_flattened_data(
+ self, image_range: None | Tuple = None, scale_data: bool = True
+ ) -> Tuple[flex.int]:
+ """
+ Image data summed along the time-of-flight direction
+ """
+
+ panel_size = self._get_image_size()
+ total_pixels = panel_size[0] * panel_size[1]
+ # Panel positions are offset by 4 in raw_data array
+ # See p24 of https://www.isis.stfc.ac.uk/Pages/sxd-user-guide6683.pdf
+ idx_offset = 4
+ max_val = None
+ num_tof_bins = len(self._get_time_of_flight())
+ raw_data = []
+ for panel_idx in range(self._get_num_panels()):
+ start_idx = (panel_idx * total_pixels) + (panel_idx * idx_offset)
+ end_idx = start_idx + total_pixels
+ panel_data = self._nxs_file["raw_data_1/detector_1/counts"][
+ 0, start_idx:end_idx, :
+ ]
+ panel_data = np.reshape(
+ panel_data, (panel_size[0], panel_size[1], num_tof_bins)
+ )
+ if image_range is not None:
+ assert (
+ len(image_range) == 2
+ ), "expected image_range to be only two values"
+ assert (
+ image_range[0] >= 0 and image_range[0] < image_range[1]
+ ), "image_range[0] out of range"
+ assert image_range[1] <= num_tof_bins, "image_range[1] out of range"
+ panel_data = np.flipud(
+ np.sum(panel_data[:, :, image_range[0] : image_range[1]], axis=2)
+ )
+ else:
+ panel_data = np.flipud(np.sum(panel_data, axis=2))
+ if panel_idx == 0 and self._panel_0_flipped():
+ panel_data = np.flipud(panel_data)
+ panel_max_val = np.max(panel_data)
+ if max_val is None or max_val < panel_max_val:
+ max_val = panel_max_val
+ raw_data.append(panel_data)
+
+ if scale_data:
+ return tuple([(i / max_val).tolist() for i in raw_data])
+
+ return tuple([i.tolist() for i in raw_data])
+
+ def get_flattened_pixel_data(
+ self, panel_idx: int, x: int, y: int
+ ) -> Tuple[Tuple, Tuple]:
+ time_channels = self._get_time_of_flight()
+ panel_size = self._get_image_size()
+ height = panel_size[1]
+ total_pixels = panel_size[0] * panel_size[1]
+ # Panel positions are offset by 4 in raw_data array
+ # See p24 of https://www.isis.stfc.ac.uk/Pages/sxd-user-guide6683.pdf
+ idx_offset = 4
+ idx = (panel_idx * total_pixels) + (panel_idx * idx_offset) + y * height + x
+ return (
+ time_channels,
+ tuple(self._nxs_file["raw_data_1/detector_1/counts"][0, idx, :].tolist()),
+ )
+
+ def get_proton_charge(self):
+ return float(self._nxs_file["raw_data_1/proton_charge"][0])