update the executable

.gitignore

@@ -105,3 +105,5 @@ ENV/
 /.downloaded
 .DS_Store
 /requirements.txt
+/examples/spectra_files/*.csv
+/examples/spectra_files/*.svg

bin/wdf-export

@@ -0,0 +1,184 @@
+#!/usr/bin/env python3
+"""Export the renishaw file as plain text files
+   usage:
+   renishaw-export  
+"""
+
+from renishawWiRE.wdfReader import WDFReader
+from argparse import ArgumentParser
+from pathlib import Path
+import os
+import sys
+import numpy as np
+import matplotlib.pyplot as plt
+import matplotlib.image as mpimg
+
+
+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=("name of the exported plain text file.\n"
+                              "If not specified, use the base name of the "
+                              ".wdf file"))
+    parser.add_argument("-f",
+                        "--format",
+                        default=".csv",
+                        help=("format of exported, valid values\n"
+                              "\t.csv (comma-separated) \n"
+                              "\t.txt (space-separated) \n"
+                              "If not specified, guess from the "
+                              "output file name.\n"
+                              "Note: -f option is ignored when "
+                              "the output file name already have an extension."))
+    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
+
+    form = args.format
+    # Try to guess the format from output output_filename
+    if args.output is not None:
+        f_ = Path(args.output).suffix
+        if len(f_) > 0:
+            form = f_
+            print("Using format {0} from output file name".format(form))
+
+    if form not in (".csv", ".txt"):
+        print("Only .csv and .txt formats are allowed! Abort.",
+              file=sys.stderr)
+        return 1
+
+    # Try to guess the
+    if form == ".csv":
+        delimiter = ","
+    else:
+        delimiter = " "
+    X, header = handle_spectra(reader, delimiter=delimiter)
+
+    # root = wdf_file.parent
+    # print(root, name)
+    if args.output is not None:
+        output_filename = Path(args.output).with_suffix(form)
+    else:
+        output_filename = wdf_file.with_suffix(form)
+
+    # output_filename = root / name
+    if not output_filename.parent.is_dir():
+        os.makedirs(output_filename.parent, exist_ok=True)
+
+    print("Extracting spectra data......")
+    try:
+        np.savetxt(output_filename, X, fmt=args.precision,
+                   delimiter=delimiter, header=header)
+    except (OSError, FileExistsError):
+        print("Output file {0} cannot be written. Abort!".
+              format(output_filename.as_posix()),
+              file=sys.stderr)
+        return 1
+
+    # There is an image associated?
+    if hasattr(reader, "img"):
+        print("Extracting mapping image......")
+        try:
+            extract_img(
+                reader, output_filename=output_filename.with_suffix(".mapping.svg"))
+        except (OSError, FileExistsError):
+            print("Image file {0} cannot be written. Abort!".
+                  format(output_filename.with_suffix(
+                      ".mapping.svg").as_posix()),
+                  file=sys.stderr)
+            return 1
+
+    return 0
+
+
+def handle_spectra(reader, delimiter=","):
+    """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 = delimiter.join(["Wavenumber", "point 1"])
+        elif len(spectra.shape) == 2:
+            # line or depth scan
+            n_p, l_w = spectra.shape
+            X = np.vstack([wn, spectra]).T
+            header = delimiter.join(["Wavenumber", ] +
+                                    ["point {:d}".format(i + 1)
+                                     for i in range(n_p)])
+        elif len(spectra.shape) == 3:
+            # mapping
+            r, c, l_w = spectra.shape
+            assert l_w == len(wn)
+            X = np.vstack([wn, spectra.reshape(r * c, l_w)]).T
+            header = delimiter.join(["Wavenumber", ] +
+                                    ["row {:d} column {:d}"
+                                     .format(i + 1,
+                                             j + 1)
+                                     for i in range(r)
+                                     for j in range(c)])
+        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
+
+
+def extract_img(reader, output_filename):
+    img = mpimg.imread(reader.img, format="jpg")
+    img_x0, img_y0 = reader.img_origins
+    img_w, img_h = reader.img_dimensions
+    map_x = reader.xpos
+    map_y = reader.ypos
+    map_w = reader.map_info["x_span"]
+    map_h = reader.map_info["y_span"]
+    plt.cla()
+    plt.figure(figsize=(10, 10))
+    plt.imshow(img, extent=(img_x0, img_x0 + img_w,
+                            img_y0 + img_h, img_y0))
+    # Add rectangle for marking
+    r = plt.Rectangle(xy=(map_x.min(), map_y.min()),
+                      width=map_w,
+                      height=map_h,
+                      fill=False)
+    plt.gca().add_patch(r)
+    plt.xlabel("Stage X [μm]")
+    plt.ylabel("Stage Y [μm]")
+    plt.savefig(output_filename)
+
+
+if __name__ == '__main__':
+    main()

setup.py

@@ -5,7 +5,7 @@
 # from setuptools.command.install import install
 
 NAME = "renishawWiRE"
-VERSION = "0.1.10"
+VERSION = "0.1.11"
 DESCRIPTION = open("README.md", encoding="utf-8").read()
 
 
@@ -60,6 +60,9 @@ def verify_version():
         "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
     ],
+    scripts=[
+        "bin/wdf-export",
+    ],
     python_requires=">=3.6",
     # cmdclass={"verify": VerifyVersionCommand},
 )