add xraydb function to compute muD

news/muD.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* function to compute mu*D based on basic information provided
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/diffpy/labpdfproc/labpdfprocapp.py

@@ -9,7 +9,7 @@
 
 def get_args(override_cli_inputs=None):
  p = ArgumentParser()
- p.add_argument("mud", help="Value of mu*D for your " "sample. Required.", type=float)
+ p.add_argument("mud", nargs="?", help="Value of mu*D for your sample.", default=None, type=float)
  p.add_argument(
  "input",
  nargs="+",
@@ -126,9 +126,14 @@ def get_args(override_cli_inputs=None):
  p.add_argument(
  "-z",
  "--z-scan-file",
- help="Path to the z-scan file to be loaded to determine the mu*D value",
+ help="Path to the z-scan file to be loaded to determine the mu*D value.",
  default=None,
  )
+ p.add_argument("--mu", help="The sample linear absorption coefficient.", default=None, type=float)
+ p.add_argument("--sample", help="The chemical formula or name of your material.", default=None)
+ p.add_argument("--energy", help="The energy in eV", default=None, type=float)
+ p.add_argument("--density", help="The material density in gr/cm^3.", default=None, type=float)
+ p.add_argument("--diameter", help="The capillary diameter in mm.", default=None, type=float)
  args = p.parse_args(override_cli_inputs)
  return args
 

src/diffpy/labpdfproc/tools.py

@@ -1,6 +1,8 @@
 import copy
 from pathlib import Path
 
+from xraydb import material_mu
+
 from diffpy.labpdfproc.mud_calculator import compute_mud
 from diffpy.utils.scattering_objects.diffraction_objects import QQUANTITIES, XQUANTITIES
 from diffpy.utils.tools import get_package_info, get_user_info
@@ -158,9 +160,9 @@ def set_xtype(args):
  return args
 
 
-def set_mud(args):
+def set_mud_from_zscan_file(args):
  """
- Set the mud based on the given input arguments
+ Set the mud based on the given z-scan file
 
  Parameters
  ----------
@@ -180,6 +182,49 @@ def set_mud(args):
  return args
 
 
+def set_mud_using_xraydb(args):
+ """
+ Set the mud using xraydb, prompting for parameters if not provided by the user
+
+ The function works in this way:
+ (1) if mu*D is provided, no further input is required, and any additional inputs are written to metadata.
+ (2) if mu*D is missing but mu is provided, prompt for diameter if missing and compute muD = mu * d.
+ (3) if neither is provided, prompt for sample name, energy, density, and diameter as needed, then compute muD.
+ Reference for the xraydb database: https://xraypy.github.io/XrayDB/python.html#xraydb.material_mu.
+
+ Parameters
+ ----------
+ args argparse.Namespace
+ the arguments from the parser
+ sample str
+ the chemical formula or name of material
+ energy float
+ the energy in eV
+ density float or None
+ material density in gr/cm^3
+ diameter float
+ the capillary diameter in mm
+
+ Returns
+ -------
+ the updated args argparse.Namespace with mu*D
+ """
+
+ if args.mud:
+ return args
+ if args.mu:
+ args.diameter = args.diameter or float(input("Please enter the capillary diameter (mm): ").strip())
+ args.mud = args.mu * args.diameter
+ return args
+ args.sample = args.sample or input("Please enter the chemical formula or name of material: ").strip()
+ args.energy = args.energy or float(input("Please enter the energy (eV): ").strip())
+ args.density = args.density or float(input("Please enter material density (gr/cm^3): ").strip())
+ args.diameter = args.diameter or float(input("Please enter the capillary diameter (mm): ").strip())
+ args.mu = material_mu(args.sample, args.energy, density=args.density, kind="total") / 10
+ args.mud = args.mu * args.diameter
+ return args
+
+
 def _load_key_value_pair(s):
  items = s.split("=")
  key = items[0].strip()
@@ -281,7 +326,8 @@ def preprocessing_args(args):
  args.output_directory = set_output_directory(args)
  args = set_wavelength(args)
  args = set_xtype(args)
- args = set_mud(args)
+ args = set_mud_from_zscan_file(args)
+ args = set_mud_using_xraydb(args)
  args = load_user_metadata(args)
  return args
 

tests/test_tools.py

@@ -13,7 +13,8 @@
  load_user_metadata,
  preprocessing_args,
  set_input_lists,
- set_mud,
+ set_mud_from_zscan_file,
+ set_mud_using_xraydb,
  set_output_directory,
  set_wavelength,
  set_xtype,
@@ -216,10 +217,10 @@ def test_set_xtype_bad():
  actual_args = set_xtype(actual_args)
 
 
-def test_set_mud(user_filesystem):
+def test_set_mud_from_zscan_file(user_filesystem):
  cli_inputs = ["2.5", "data.xy"]
  actual_args = get_args(cli_inputs)
- actual_args = set_mud(actual_args)
+ actual_args = set_mud_from_zscan_file(actual_args)
  assert actual_args.mud == pytest.approx(2.5, rel=1e-4, abs=0.1)
  assert actual_args.z_scan_file is None
 
@@ -230,16 +231,41 @@ def test_set_mud(user_filesystem):
  expected = [3, str(test_dir / "testfile.xy")]
  cli_inputs = ["2.5", "data.xy"] + inputs
  actual_args = get_args(cli_inputs)
- actual_args = set_mud(actual_args)
+ actual_args = set_mud_from_zscan_file(actual_args)
  assert actual_args.mud == pytest.approx(expected[0], rel=1e-4, abs=0.1)
  assert actual_args.z_scan_file == expected[1]
 
 
-def test_set_mud_bad():
+def test_set_mud_from_zscan_file_bad():
  cli_inputs = ["2.5", "data.xy", "--z-scan-file", "invalid file"]
  actual_args = get_args(cli_inputs)
  with pytest.raises(FileNotFoundError, match="Cannot find invalid file. Please specify a valid file path."):
- actual_args = set_mud(actual_args)
+ actual_args = set_mud_from_zscan_file(actual_args)
+
+
+params_mud = [
+ # user specified mud
+ (["0.7952", "data.xy"], [""]),
+ # user specified mu but not mud
+ (["data.xy", "--mu", "1.2522", "--diameter", "0.635"], [""]),
+ (["data.xy", "--mu", "1.2522"], ["0.635"]),
+ # user did not specify mud or mu
+ (["data.xy"], ["ZrO2", "17445", "1.009", "0.635"]),
+ (["data.xy", "--energy", "17445", "--density", "1.009", "--diameter", "0.635"], ["ZrO2"]),
+ (["data.xy", "--sample", "ZrO2", "--density", "1.009", "--diameter", "0.635"], ["17445.362740959618"]),
+ (["data.xy", "--sample", "ZrO2", "--energy", "17445", "--diameter", "0.635"], ["1.009"]),
+ (["data.xy", "--sample", "ZrO2", "--energy", "17445", "--density", "1.009"], ["0.635"]),
+ (["data.xy", "--sample", "ZrO2", "--energy", "17445", "--density", "1.009", "--diameter", "0.635"], [""]),
+]
+
+
+@pytest.mark.parametrize("cli_inputs, user_inputs", params_mud)
+def test_set_mud_using_xraydb(cli_inputs, user_inputs, monkeypatch):
+ inp_iter = iter(user_inputs)
+ monkeypatch.setattr("builtins.input", lambda _: next(inp_iter))
+ actual_args = get_args(cli_inputs)
+ actual_args = set_mud_using_xraydb(actual_args)
+ assert actual_args.mud == pytest.approx(0.7952, rel=1e-4, abs=0.1)
 
 
 params5 = [