Merge pull request #2 from sbillinge/app_work

working version of app, then broken again after adding diffraction ob…

Author: sbillinge

diffpy/labpdfproc/_version.py

@@ -16,6 +16,7 @@
 import sys
 
 
+
 def get_keywords():
     """Get the keywords needed to look up the version information."""
     # these strings will be replaced by git during git-archive.

diffpy/labpdfproc/functions.py

@@ -0,0 +1,16 @@
+import numpy as np
+
+wavelengths = {"Mo": 0.7107, "Ag": 0.59}
+def compute_cve(diffraction_data, mud, wavelength):
+    # for a given mu and d and lambda, we will compute cve on a tth grid
+    # something arbitrary for the moment
+    cve = diffpy.utils.DiffractionObject()
+    cve_x = diffraction_data.on_tth[0]
+    cve_y = cve_x * mud * wavelength
+    cve.insert_scattering_quantity(cve_x, cve_y, "tth", metadata={ })
+    return cve
+
+def apply_corr(i_m, cve):
+    # we apply the absorption correction by doing: I(tth) * c_ve
+    i_c = i_m * cve
+    return i_c

diffpy/labpdfproc/labpdfprocapp.py

@@ -1,9 +1,11 @@
 import sys
-import numpy as np
-from labpdfproc.functions import compute_cve, apply_corr
-from diffpy.utils.parsers.loaddata import loadData
 from argparse import ArgumentParser
 
+from diffpy.labpdfproc.functions import compute_cve, apply_corr, wavelengths
+from diffpy.utils.parsers.loaddata import loadData
+from diffpy.utils.scattering_objects import DiffractionObject
+
+
 known_sources = ["Ag", "Mo"]
 # def load_data(input_file):
 #     # we want to load .xy, xye, file types. These are the most common. For anyting else (.snc, .txt, .csv, .dat) we return an error message. Why: some of them have different delimineters.
@@ -19,7 +21,6 @@
 #     else:
 #         raise ValueError('Error: your .xy contains headers. Delete the header rows in your .xy or .xye file')
 
-
 # def tth_to_q(tth, wl):
 #     tth_rad = np.deg2rad(tth)
 #     q = (4 * np.pi / wl) * np.sin(tth_rad / 2)
@@ -34,8 +35,8 @@
 
 def get_args():
     p = ArgumentParser()
-    p.add_argument("filename", help="the filename of the datafile to load")
-    p.add_argument("mud", help="mu*D for your sample")
+    p.add_argument("data_file", help="the filename of the datafile to load")
+    p.add_argument("mud", help="mu*D for your sample", type=float)
     p.add_argument("--anode_type", help=f"x-ray source, allowed values:{*[known_sources],}", default="Mo")
     args = p.parse_args()
     return args
@@ -49,19 +50,21 @@ def main():
         print('usage: labpdfproc <input_file> <mu> <diameter> <lambda>')
 
     args = get_args()
-    print(args.__dir__)
-    tth, i_m = loadData(input_file, unpack=True)
+    wavelength = wavelengths[args.anode_type]
+    input_pattern = DiffractionObject()
+    xarray, yarray = loadData(args.data_file, unpack=True)
+    input_pattern.insert_scattering_quantity(xarray, yarray, "tth", metadata={ })
 
-    cve = compute_cve(tth, mu, diameter, wl)
-    i_c = apply_corr(i_m, cve)
-    q = tth_to_q(tth, wl)
+    cve = compute_cve(input_pattern, args.mud, wavelength)
+    i_c = input_pattern * cve
 
     # get the basename from the input_file and save the corrected patter as a .tth and a .chi file.
-    base_name = input_file.split('.')[0]
-    output_chi = f"{base_name}.chi"
-    output_tth = f"{base_name}.tth"
-    np.savetxt(output_tth, np.column_stack((tth, i_c)), header='tth I(tth)')
-    np.savetxt(output_chi, np.column_stack((q, i_c)), header='tth I(tth)')
+    # base_name = input_file.split('.')[0]
+    # output_chi = f"{base_name}.chi"
+    # output_tth = f"{base_name}.tth"
+    # np.savetxt(output_tth, np.column_stack((tth, i_c)), header='tth I(tth)')
+    # np.savetxt(output_chi, np.column_stack((q, i_c)), header='tth I(tth)')
+    input_pattern.dump("filename", type="chi")
 
 if __name__ == '__main__':
-    main()
+    main()