XFEL small molecule improvements

xfel/small_cell/command_line/powder_from_spots.py

@@ -95,6 +95,9 @@
     .type = space_group
     .help = Show positions of miller indices from this unit_cell and space \
             group. Not implemented.
+  n_max = None
+    .type = int
+    .help = Stop plotting after this many experiments.
 filter {
   enable = False
     .type = bool
@@ -121,6 +124,10 @@
     .type = str
   xy_file = None
     .type = str
+  xy_file_units = *d q
+    .type = choice
+    .help = X-axis units for xy_file output: d-spacing in Angstroms (default) \
+            or inverse-d-spacing (q) in inverse Angstroms.
   peak_file = None
     .type = str
     .help = Optionally, specify an output file for interactive peak picking in \
@@ -139,9 +146,21 @@
     .type = float
   d_max = None
     .type = float
+  q_min = None
+    .type = float
+    .help = Minimum q (inverse angstroms). Converted to d_max if provided.
+  q_max = None
+    .type = float
+    .help = Maximum q (inverse angstroms). Converted to d_min if provided.
   step_px = None
     .type = float
     .multiple = True
+  d_target = None
+    .type = float
+    .help = If set, enables detector distance refinement along z-axis
+  q_target = None
+    .type = float
+    .help = Target q value (inverse angstroms). Converted to d_target if provided.
 }
 plot {
   interactive = True
@@ -185,11 +204,33 @@ def run(self):
     experiments = params.input.experiments[0].data
     reflections = params.input.reflections[0].data
 
+    # Convert q parameters to d parameters if needed (q = 1/d)
+    if params.center_scan.q_min is not None:
+      params.center_scan.d_max = 1.0 / params.center_scan.q_min
+    if params.center_scan.q_max is not None:
+      params.center_scan.d_min = 1.0 / params.center_scan.q_max
+    if params.center_scan.q_target is not None:
+      params.center_scan.d_target = 1.0 / params.center_scan.q_target
+
     if params.center_scan.d_min:
       assert params.center_scan.d_max
       cscan = Center_scan(experiments, reflections, params)
+
+      # First XY refinement sequence
       for step in params.center_scan.step_px:
         cscan.search_step(step)
+
+      # Z-axis refinement if d_target is set
+      if params.center_scan.d_target is not None:
+        # Default Z steps in microns
+        z_steps_um = [4000, 2000, 1000, 500, 250, 125, 80, 40, 20, 10, 5]
+        for step_um in z_steps_um:
+          cscan.search_step_z(step_um, params.center_scan.d_target)
+
+        # Second XY refinement sequence
+        for step in params.center_scan.step_px:
+          cscan.search_step(step)
+
       if params.output.geom_file is not None:
         experiments.as_file(params.output.geom_file)
 

xfel/small_cell/command_line/powder_refine_geometry.py

@@ -0,0 +1,158 @@
+# LIBTBX_SET_DISPATCHER_NAME cctbx.xfel.powder_refine_geometry
+from __future__ import division
+import logging
+
+from iotbx.phil import parse
+from dials.util import log
+from dials.util import show_mail_on_error
+from dials.util.options import ArgumentParser
+from xfel.small_cell.geometry_refiner import PowderGeometryRefiner
+
+
+logger = logging.getLogger("dials.command_line.powder_refine_geometry")
+
+help_message = """
+Refine detector geometry using powder diffraction d-spacings.
+
+Examples of usage:
+
+# Basic usage with defaults (LaB6)
+$ cctbx.xfel.powder_refine_geometry spots.expt spots.refl
+
+# Custom d-spacings (e.g., for Si standard)
+$ cctbx.xfel.powder_refine_geometry spots.expt spots.refl \\
+    reference_d_spacings=3.135,1.920,1.637,1.357
+
+# Or use unit cell and space group instead
+$ cctbx.xfel.powder_refine_geometry spots.expt spots.refl \\
+    unit_cell=4.156,4.156,4.156,90,90,90 space_group=Pm-3m
+
+# Refine only XY shift (fix distance and tilt)
+$ cctbx.xfel.powder_refine_geometry spots.expt spots.refl \\
+    refine.distance=False refine.tilt=False
+
+# Specify output file
+$ cctbx.xfel.powder_refine_geometry spots.expt spots.refl \\
+    output.experiments=calibrated.expt
+
+This tool uses spotfinding output from a powder standard with known d-spacings
+to refine detector geometry. It optimizes a 5-parameter detector model:
+- distance: shift along detector normal
+- shift1/shift2: XY shifts along fast/slow axes
+- tau2/tau3: tilts around fast/slow axes
+
+The refinement minimizes the sum of squared differences between observed
+d-spacings and the nearest reference d-spacing.
+
+Default reference d-spacings are for LaB6 (SRM 660):
+  4.156 A (100), 2.939 A (110), 2.399 A (111), 2.078 A (200), 1.858 A (210)
+"""
+
+phil_scope = parse(
+    """
+reference_d_spacings = 4.156 2.939 2.399 2.078 1.858
+  .type = floats
+  .help = Reference d-spacings in Angstroms. Default: first 5 LaB6 peaks. \
+          Either use this OR specify unit_cell and space_group.
+
+unit_cell = None
+  .type = unit_cell
+  .help = Unit cell to generate reference d-spacings (use with space_group). \
+          If specified, this overrides reference_d_spacings.
+
+space_group = None
+  .type = space_group
+  .help = Space group to generate reference d-spacings (use with unit_cell). \
+          If specified, this overrides reference_d_spacings.
+
+d_min = 1.5
+  .type = float
+  .help = Minimum d-spacing to include in refinement
+
+d_max = 20
+  .type = float
+  .help = Maximum d-spacing to include in refinement
+
+max_distance_inv_ang = 0.002
+  .type = float
+  .help = Maximum distance from reference d-spacing in inverse Angstroms. \
+          Reflections further than this from any reference will be excluded.
+
+refine {
+  distance = True
+    .type = bool
+    .help = Refine detector distance along normal
+  shift = True
+    .type = bool
+    .help = Refine XY shift (shift1 and shift2)
+  tilt = True
+    .type = bool
+    .help = Refine detector tilts (tau2 and tau3)
+}
+
+output {
+  experiments = refined.expt
+    .type = path
+    .help = Output filename for refined experiments
+  log = powder_refine_geometry.log
+    .type = path
+    .help = Output log file
+}
+"""
+)
+
+
+class Script(object):
+    def __init__(self):
+        usage = "$ cctbx.xfel.powder_refine_geometry EXPERIMENTS REFLECTIONS [options]"
+        self.parser = ArgumentParser(
+            usage=usage,
+            phil=phil_scope,
+            epilog=help_message,
+            check_format=False,
+            read_reflections=True,
+            read_experiments=True,
+        )
+
+    def run(self):
+        params, options = self.parser.parse_args(show_diff_phil=True)
+
+        # Validate input
+        if len(params.input.experiments) != 1 or len(params.input.reflections) != 1:
+            raise ValueError("Please provide exactly one experiments file and "
+                             "one reflections file")
+
+        experiments = params.input.experiments[0].data
+        reflections = params.input.reflections[0].data
+
+        print(f"\nLoaded {len(experiments)} experiments with "
+              f"{len(reflections)} reflections")
+
+        if params.unit_cell is not None and params.space_group is not None:
+            print(f"Using unit_cell: {params.unit_cell}")
+            print(f"Using space_group: {params.space_group}")
+        else:
+            print(f"Reference d-spacings: {params.reference_d_spacings}")
+
+        # Create and run refiner
+        refiner = PowderGeometryRefiner(experiments, reflections, params)
+        result = refiner.run()
+
+        if result is not None:
+            # Report final geometry
+            refiner.report_geometry_changes()
+
+            # Save refined experiments
+            refined_experiments = refiner.get_refined_experiments()
+            print(f"\nSaving refined experiments to {params.output.experiments}")
+            refined_experiments.as_file(params.output.experiments)
+
+            print("\nRefinement complete.")
+        else:
+            print("\nNo refinement performed.")
+
+
+if __name__ == "__main__":
+    with show_mail_on_error():
+        script = Script()
+        script.run()