From 783aa73667230cd2746d70f7dcd696420caed0e2 Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Mon, 29 Apr 2024 10:10:00 -0400
Subject: [PATCH 1/2] initial commit of loading all readable files if not
 specified

---
 src/diffpy/labpdfproc/labpdfprocapp.py | 71 +++++++++++++++-----------
 1 file changed, 40 insertions(+), 31 deletions(-)

diff --git a/src/diffpy/labpdfproc/labpdfprocapp.py b/src/diffpy/labpdfproc/labpdfprocapp.py
index 93b57b2..63b0139 100644
--- a/src/diffpy/labpdfproc/labpdfprocapp.py
+++ b/src/diffpy/labpdfproc/labpdfprocapp.py
@@ -1,3 +1,4 @@
+import glob
 import sys
 from argparse import ArgumentParser
 from pathlib import Path
@@ -63,41 +64,49 @@ def get_args():
 def main():
     args = get_args()
     wavelength = WAVELENGTHS[args.anode_type]
-    filepath = Path(args.input_file)
-    outfilestem = filepath.stem + "_corrected"
-    corrfilestem = filepath.stem + "_cve"
-    outfile = Path(outfilestem + ".chi")
-    corrfile = Path(corrfilestem + ".chi")
+    input_dir = Path.cwd()
+    if args.input_file:
+        filepath = Path(args.input_file)
+        input_dir = Path.cwd() / filepath.parent
 
-    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_files = glob.glob(str(input_dir) + "/*", recursive=True)
+    filepaths = [Path(file) for file in input_files]
 
-    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},
-    )
+    for filepath in filepaths:
+        outfilestem = filepath.stem + "_corrected"
+        corrfilestem = filepath.stem + "_cve"
+        outfile = Path(outfilestem + ".chi")
+        corrfile = Path(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"
+            )
+
+        input_pattern = Diffraction_object(wavelength=wavelength)
+        xarray, yarray = loadData(filepath.name, 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")
+        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 args.output_correction:
+            absorption_correction.dump(f"{corrfile}", xtype="tth")
 
 
 if __name__ == "__main__":

From b07789232713d44f9523605afa12fad9393357f3 Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Mon, 29 Apr 2024 16:14:51 -0400
Subject: [PATCH 2/2] skip non-readable files using loadData

---
 src/diffpy/labpdfproc/labpdfprocapp.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/diffpy/labpdfproc/labpdfprocapp.py b/src/diffpy/labpdfproc/labpdfprocapp.py
index 63b0139..2e436c7 100644
--- a/src/diffpy/labpdfproc/labpdfprocapp.py
+++ b/src/diffpy/labpdfproc/labpdfprocapp.py
@@ -90,7 +90,12 @@ def main():
             )
 
         input_pattern = Diffraction_object(wavelength=wavelength)
-        xarray, yarray = loadData(filepath.name, unpack=True)
+        try:
+            xarray, yarray = loadData(filepath, unpack=True)
+        except Exception as e:
+            print(f"Non-readable data file {filepath}: {e}")
+            continue
+
         input_pattern.insert_scattering_quantity(
             xarray,
             yarray,