load input directory and files

src/diffpy/labpdfproc/labpdfprocapp.py

@@ -3,7 +3,13 @@
 from pathlib import Path
 
 from diffpy.labpdfproc.functions import apply_corr, compute_cve
-from diffpy.labpdfproc.tools import known_sources, load_user_metadata, set_output_directory, set_wavelength
+from diffpy.labpdfproc.tools import (
+    known_sources,
+    load_user_metadata,
+    set_input_files,
+    set_output_directory,
+    set_wavelength,
+)
 from diffpy.utils.parsers.loaddata import loadData
 from diffpy.utils.scattering_objects.diffraction_objects import XQUANTITIES, Diffraction_object
 
@@ -76,45 +82,52 @@ def get_args(override_cli_inputs=None):
 
 def main():
     args = get_args()
+    args = set_input_files(args)
     args.output_directory = set_output_directory(args)
     args.wavelength = set_wavelength(args)
     args = load_user_metadata(args)
 
-    filepath = Path(args.input_file)
-    outfilestem = filepath.stem + "_corrected"
-    corrfilestem = filepath.stem + "_cve"
-    outfile = args.output_directory / (outfilestem + ".chi")
-    corrfile = args.output_directory / (corrfilestem + ".chi")
+    for input_file in args.input_file:
+        filepath = Path(args.input_file)
+        outfilestem = filepath.stem + "_corrected"
+        corrfilestem = filepath.stem + "_cve"
+        outfile = args.output_directory / (outfilestem + ".chi")
+        corrfile = args.output_directory / (corrfilestem + ".chi")
 
-    if outfile.exists() and not args.force_overwrite:
-        sys.exit(
-            f"Output file {str(outfile)} already exists. Please rerun "
-            f"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 "
-            f"exists. Please rerun specifying -f if you want to overwrite it."
-        )
+        if outfile.exists() and not args.force_overwrite:
+            sys.exit(
+                f"Output file {str(outfile)} already exists. Please rerun "
+                f"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 "
+                f"exists. Please rerun specifying -f if you want to overwrite it."
+            )
 
-    input_pattern = Diffraction_object(wavelength=args.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},
-    )
+        input_pattern = Diffraction_object(wavelength=args.wavelength)
+
+        try:
+            xarray, yarray = loadData(args.input_file, unpack=True)
+        except Exception as e:
+            raise ValueError(f"Failed to load data from {filepath}: {e}.")
+
+        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, args.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")
+        absorption_correction = compute_cve(input_pattern, args.mud, args.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 args.output_correction:
+            absorption_correction.dump(f"{corrfile}", xtype="tth")
 
 
 if __name__ == "__main__":

src/diffpy/labpdfproc/tests/test_tools.py

@@ -4,7 +4,50 @@
 import pytest
 
 from diffpy.labpdfproc.labpdfprocapp import get_args
-from diffpy.labpdfproc.tools import known_sources, load_user_metadata, set_output_directory, set_wavelength
+from diffpy.labpdfproc.tools import (
+    known_sources,
+    load_user_metadata,
+    set_input_files,
+    set_output_directory,
+    set_wavelength,
+)
+from diffpy.utils.parsers.loaddata import loadData
+
+params1 = [
+    (
+        ["--input-file", "."],
+        [
+            ".",
+            ["good_data.chi", "good_data.xy", "good_data.txt", "unreadable_file.txt", "binary.pkl"],
+        ],
+    ),
+    (["--input-file", "good_data.chi"], [".", "good_data.chi"]),
+    (["--input-file", "input_dir/unreadable_file.txt"], ["input_dir", "unreadable_file.txt"]),
+    # ([Path.cwd()], [Path.cwd()]),
+]
+
+
+@pytest.mark.parametrize("inputs, expected", params1)
+def test_set_input_files(inputs, expected, user_filesystem):
+    expected_input_directory = Path(user_filesystem) / expected[0]
+    expected_input_files = expected[1]
+
+    cli_inputs = ["2.5"] + inputs
+    actual_args = get_args(cli_inputs)
+    actual_args = set_input_files(actual_args)
+    assert actual_args.input_directory == expected_input_directory
+    assert set(actual_args.input_file) == set(expected_input_files)
+
+
+def test_loadData_with_input_files(user_filesystem):
+    xarray_chi, yarray_chi = loadData("good_data.chi", unpack=True)
+    xarray_xy, yarray_xy = loadData("good_data.xy", unpack=True)
+    xarray_txt, yarray_txt = loadData("good_data.txt", unpack=True)
+    with pytest.raises(ValueError):
+        xarray_txt, yarray_txt = loadData("unreadable_file.txt", unpack=True)
+    with pytest.raises(ValueError):
+        xarray_pkl, yarray_pkl = loadData("binary.pkl", unpack=True)
+
 
 params1 = [
     ([], ["."]),

src/diffpy/labpdfproc/tools.py

@@ -1,9 +1,41 @@
+import glob
+import os
 from pathlib import Path
 
 WAVELENGTHS = {"Mo": 0.71, "Ag": 0.59, "Cu": 1.54}
 known_sources = [key for key in WAVELENGTHS.keys()]
 
 
+def set_input_files(args):
+    """
+    Set input directory and files
+
+    Parameters
+    ----------
+    args argparse.Namespace
+        the arguments from the parser
+
+    Returns
+    -------
+    args argparse.Namespace
+
+    """
+    if not args.input_file or not Path(args.input_file).exists():
+        raise ValueError("Please specify valid input file or directory.")
+
+    if not Path(args.input_file).is_dir():
+        input_dir = Path.cwd() / Path(args.input_file).parent
+        input_file_name = Path(args.input_file).name
+        args.input_file = input_file_name
+    else:
+        input_dir = Path(args.input_file).resolve()
+        input_files = [file for file in glob.glob(str(input_dir) + "/*", recursive=True) if os.path.isfile(file)]
+        input_file_names = [os.path.basename(input_file_path) for input_file_path in input_files]
+        args.input_file = input_file_names
+    setattr(args, "input_directory", input_dir)
+    return args
+
+
 def set_output_directory(args):
     """
     set the output directory based on the given input arguments