first iteration of functional app

diffpy/labpdfproc/labpdfprocapp.py

@@ -0,0 +1,67 @@
+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
+
+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.
+#     # we want to load the tth column in a numpy array 
+#     # we want to load the intensitie Im into a numpy array
+#     # the input files should not contain any header. Typically, .xy or .xye files don't contain headers.
+#     tth = np.loadtxt(input_file, usecols=0)
+#     i_m = np.loadtxt(input_file, usecols=1)
+#     # this should return an error if the first row contains anything except a float, and if the columns are not separated by a space. 
+#     # I think the latter is also dealt with if we check if the first elemnt in one tth is a flaot.
+#     if np.issubdtype(tth[0], np.floating) and np.issubdtype(i_m[0], np.floating):
+#         return tth, i_m
+#     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)
+#     return q
+
+
+
+# def write_files(base_name):
+    # we save the corrected intensities in a two-column file on a q-grid and a tth-grid.
+    # we need to know the x-ray wavelenth so that we can convert tth to q
+    # we make a new two-column file .chi where column 1 contains the q grid and columnt 2 contains the corrected intensities.
+
+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("--anode_type", help=f"x-ray source, allowed values:{*[known_sources],}", default="Mo")
+    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()
+    print(args.__dir__)
+    tth, i_m = loadData(input_file, unpack=True)
+
+    cve = compute_cve(tth, mu, diameter, wl)
+    i_c = apply_corr(i_m, cve)
+    q = tth_to_q(tth, wl)
+
+    # 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)')
+
+if __name__ == '__main__':
+    main()

setup.py

@@ -1,10 +1,13 @@
 import sys
+import os
 from os import path
 
 from setuptools import find_packages, setup
 
 import versioneer
 
+MYDIR = os.path.dirname(os.path.abspath(__file__))
+
 # NOTE: This file must remain Python 2 compatible for the foreseeable future,
 # to ensure that we error out properly for people with outdated setuptools
 # and/or pip.
@@ -48,20 +51,20 @@
     author_email="sb2896@columbia.edu",
     url="https://github.com/sbillinge/diffpy.labpdfproc",
     python_requires=">={}".format(".".join(str(n) for n in min_version)),
-    packages=find_packages(exclude=["docs", "tests"]),
+    packages=find_packages(os.path.join(MYDIR, "diffpy"), exclude=["docs", "tests"]),
     entry_points={
         "console_scripts": [
-            'labpdfproc = diffpy.snmf.stretchednmfapp:main',
+            'labpdfproc = diffpy.labpdfproc.labpdfprocapp:main',
         ],
     },
     include_package_data=True,
-    package_data={
-        "labpdfproc": [
-            # When adding files here, remember to update MANIFEST.in as well,
-            # or else they will not be included in the distribution on PyPI!
-            # 'path/to/data_file',
-        ]
-    },
+    # package_data={
+    #     "labpdfproc": [
+    #         # When adding files here, remember to update MANIFEST.in as well,
+    #         # or else they will not be included in the distribution on PyPI!
+    #         # 'path/to/data_file',
+    #     ]
+    # },
     install_requires=requirements,
     license="BSD (3-clause)",
     classifiers=[