initial working example of executable

bin/renishaw-export.py

@@ -0,0 +1,125 @@
+#!/usr/bin/env python3
+"""Export the renishaw file as plain text files
+   usage:
+   renishaw-export  
+"""
+
+from renishawWiRE.wdfReader import WDFReader
+from renishawWiRE.types import MeasurementType
+from argparse import ArgumentParser
+from pathlib import Path
+import os
+import sys
+import numpy as np
+
+
+def main():
+    parser = ArgumentParser(description=("Simple script to convert Renishaw wdf spectroscopy"
+                                         " files into plain text files"))
+    parser.add_argument("wdf_file",
+                        help="Renishaw wdf for input")
+    parser.add_argument("-o",
+                        "--output",
+                        default=None,
+                        help=("base name for the exported files."
+                              " Do not need to add extension"))
+    parser.add_argument("-f",
+                        "--format",
+                        default=".csv",
+                        help=("format of exported, valid values\n"
+                              ".csv (comma-separated) "
+                              ".txt (space-separated)"))
+    parser.add_argument("-p",
+                        "--precision",
+                        default="%.4f",
+                        help=("precision of exported data."
+                              " Use printf-compatible format such as %2.4f."))
+
+    args = parser.parse_args()
+    wdf_file = Path(args.wdf_file).expanduser().resolve()
+    if not wdf_file.is_file():
+        print("The file {0} does not exist. Abort!".format(wdf_file.as_posix()),
+              file=sys.stderr)
+        return 1
+
+    reader = WDFReader(wdf_file)
+    # Output test information
+    print("Your Renishaw file looks like:")
+    reader.print_info()
+    # handle the spectra data
+    X, header = handle_spectra(reader)
+
+    if args.format not in (".csv", ".txt"):
+        print("Only csv and txt formats are allowed! Abort.", file=sys.stderr)
+        return 1
+    if args.format == ".csv":
+        delimiter = ","
+    else:
+        delimiter = " "
+
+    root = wdf_file.parent
+    # print(root, name)
+    if args.output is not None:
+        name = Path(args.output).with_suffix(args.format)
+    else:
+        name = wdf_file.with_suffix(args.format)
+
+    filename = root / name
+    if not filename.parent.is_dir():
+        os.makedirs(filename.parent, exist_ok=True)
+
+    np.savetxt(filename, X, fmt=args.precision,
+               delimiter=delimiter, header=header)
+
+    return 0
+
+
+def handle_spectra(reader):
+    """Function to treat single point spectrum
+       return the X matrix using numpy, and header
+    """
+    # Wavenumber is alwa
+    wn = reader.xdata
+    spectra = reader.spectra
+    try:
+        if len(spectra.shape) == 1:
+            # single point
+            l_w, = spectra.shape
+            assert l_w == len(wn)
+            X = np.vstack([wn, spectra]).T
+            header = "Wavenumber,point 1"
+            print(1, X)
+        elif len(spectra.shape) == 2:
+            # line or depth scan
+            n_p, l_w = spectra.shape
+            X = np.vstack([wn, spectra]).T
+            header = "Wavenumber," + ",".join(["point {:d}".format(i + 1)
+                                               for i in range(n_p)])
+            print(2, X)
+        elif len(spectra.shape) == 3:
+            # mapping
+            c, r, l_w = spectra.shape
+            assert l_w == len(wn)
+            X = np.vstack([wn, spectra.reshape(c * r, l_w)]).T
+            header = "Wavenumber," + ",".join(["row {:d} column {:d}"
+                                               .format(i + 1,
+                                                       j + 1)
+                                               for i in range(c)
+                                               for j in range(r)])
+            print(3, X)
+        else:
+            print(("There seems to be something wrong "
+                   "with the spectral file. Abort!"),
+                  file=sys.stderr)
+            return 1
+    except AssertionError:
+        print(("The length of wavenumber points do not "
+               "match that in the spectral data. Abort!"), file=sys.stderr)
+
+    # Sort the ndarray according to 0st
+    X = X[X[:, 0].argsort()]
+    return X, header
+
+
+if __name__ == '__main__':
+    main()