3m releasable version working

diffpy/labpdfproc/functions.py

@@ -209,7 +209,12 @@ def compute_cve(diffraction_data, mud, wavelength):
     orig_grid = diffraction_data.on_tth[0]
     newcve = np.interp(orig_grid, TTH_GRID, cve)
     abdo = Diffraction_object(wavelength=wavelength)
-    abdo.insert_scattering_quantity(orig_grid, newcve, "tth")
+    abdo.insert_scattering_quantity(orig_grid, newcve, "tth",
+                                    metadata=diffraction_data.metadata,
+                                    name=f"absorption correction, cve, for {diffraction_data.name}",
+                                    wavelength=diffraction_data.wavelength,
+                                    scat_quantity="cve"
+                                    )
 
     return abdo
 
@@ -234,8 +239,3 @@ def apply_corr(diffraction_pattern, absorption_correction):
     corrected_pattern = diffraction_pattern * absorption_correction
     return corrected_pattern
 
-
-# to be added in diffpy.utils
-# def dump(base_name, do):
-#    data_to_save = np.column_stack((do.on_tth[0], do.on_tth[1]))
-#    np.savetxt(f'{base_name}_proc.chi', data_to_save)

diffpy/labpdfproc/labpdfprocapp.py

@@ -1,5 +1,6 @@
 import sys
 from argparse import ArgumentParser
+from pathlib import Path
 
 import numpy as np
 from diffpy.labpdfproc.functions import compute_cve, apply_corr
@@ -18,30 +19,42 @@ def get_args():
     p.add_argument("-w", "--wavelength", help=f"X-ray source wavelength. Not needed if the anode-type is specified. This will override the wavelength if anode type is specified", default=None, type=float)
     p.add_argument("-o", "--output-directory", help=f"the name of the output directory. If it doesn't exist it will be created.  Not currently implemented", default=None)
     p.add_argument("-x", "--xtype", help=f"the quantity on the independnt variable axis. allowed values:{*XQUANTITIES,}. If not specified then two-theta is assumed for the independent variable. Only implemented for tth currently", default="tth")
+    p.add_argument("-c", "--output-correction", action='store_true', help=f"the quantity on the independnt variable axis. allowed values:{*XQUANTITIES,}. If not specified then two-theta is assumed for the independent variable. Only implemented for tth currently", default="tth")
+    p.add_argument("-f", "--force-overwrite", action='store_true', help="outputs will not overwrite existing file unless --force is spacified")
     args = p.parse_args()
     return args
 
 
 def main():
-    # we want the user to type the following:
-    # labpdfproc <input_file> <mu> <diameter> <Ag, ag, Mo, mo, Cu, cu>
-
-    # if they give less or more than 4 positional arguments, we return an error message.
-    if len(sys.argv) < 4:
-        print("usage: labpdfproc <input_file> <mu> <diameter> <lambda>")
-
     args = get_args()
     wavelength = WAVELENGTHS[args.anode_type]
-    input_pattern = Diffraction_object(wavelength=wavelength)
-    xarray, yarray = loadData(args.input_file, unpack=True)
-    input_pattern.insert_scattering_quantity(xarray, yarray, "tth")
+    filepath = Path(args.input_file)
+    outfilestem = filepath.stem + "_corrected"
+    corrfilestem = filepath.stem + "_cve"
+    outfile = Path(outfilestem + ".chi")
+    corrfile = Path(corrfilestem + ".chi")
 
-    abdo = compute_cve(input_pattern, args.mud, wavelength)
-    abscormodo = apply_corr(input_pattern, abdo)
+    if outfile.exists() and not args.force_overwrite:
+        sys.exit(f"output file {str(outfile)} already exists. Please rerun specifying -f if you want to overwrite it")
+    if corrfile.exists() and args.output_correction and not args.force_overwrite:
+        sys.exit(f"corrections file {str(corrfile)} was requested and already exists. Please rerun specifying -f if you want to overwrite it")
 
-    base_name = args.input_file.split(".")[0]
-    data_to_save = np.column_stack((abscormodo.on_tth[0], abscormodo.on_tth[1]))
-    np.savetxt(f"{base_name}_proc.chi", data_to_save)
+    input_pattern = Diffraction_object(wavelength=wavelength)
+    xarray, yarray = loadData(args.input_file, unpack=True)
+    input_pattern.insert_scattering_quantity(xarray, yarray, "tth",
+                                             scat_quantity="x-ray",
+                                             name=str(args.input_file),
+                                             metadata={"muD": args.mud,
+                                                       "anode_type": args.anode_type}
+                                             )
+
+    absorption_correction = compute_cve(input_pattern, args.mud, wavelength)
+    corrected_data = apply_corr(input_pattern, absorption_correction)
+    corrected_data.name = f"Absorption corrected input_data: {input_pattern.name}"
+    corrected_data.dump(f"{outfile}", xtype="tth")
+
+    if args.output_correction:
+        absorption_correction.dump(f"{corrfile}", xtype="tth")
 
 
 if __name__ == "__main__":

requirements-dev.txt

@@ -5,6 +5,7 @@ codecov
 coverage
 flake8
 isort
+metadata
 nbstripout
 pre-commit
 pre-commit-hooks

requirements.txt

@@ -1,3 +1,4 @@
 # List required packages in this file, one per line.
 numpy
+pathlib
 diffpy.utils