docs: add hologram file conversion example

.gitignore

@@ -105,3 +105,4 @@ _version_save.py
 *.bib.bak
 examples/*.tif
 examples/*.hdf5
+.pytest_cache

docs/examples.rst

@@ -11,3 +11,5 @@ Examples
 .. fancy_include:: hyperspy_hologram.py
 
 .. fancy_include:: convert_txt2npy.py
+
+.. fancy_include:: convert_txt2tif.py

examples/convert_txt2npy.py

@@ -9,7 +9,7 @@ class for a very unique data set. In this example, QPI data,
 
 This example must be executed with a directory as an
 command line argument, i.e.
-``python convert_tcxt2tig /path/to/folder/``
+``python convert_txt2npy /path/to/folder/``
 """
 import pathlib
 import sys

examples/convert_txt2tif.py

@@ -0,0 +1,58 @@
+"""Conversion of external holograms to .tif files
+
+Qpformat can load hologram data from .tif image files. If your
+experimental hologram data are stored in a different file format,
+you can either request its implementation in qpformat by
+`creating an issue<https://github.com/RI-imaging/qpformat/issues/new>`_
+or you can modify this example script to your needs.
+
+This example must be executed with a directory as an
+command line argument, i.e.
+``python convert_txt2tif /path/to/folder/``
+"""
+import pathlib
+import sys
+
+import numpy as np
+from skimage.external import tifffile
+
+# File names ending with these strings are ignored
+ignore_endswith = ['.bmp', '.npy', '.opj', '.png', '.pptx', '.py', '.svg',
+                   '.tif', '.txt', '_RIdist', '_parameter', '_parameter_old',
+                   '_phase', 'n_array', 'n_array_real', '~']
+
+
+def get_paths(folder, ignore_endswith=ignore_endswith):
+    """Return hologram file paths
+
+    Parameters
+    ----------
+    folder: str or pathlib.Path
+        Path to search folder
+    ignore_endswith: list
+        List of filename ending strings indicating which
+        files should be ignored.
+    """
+    folder = pathlib.Path(folder).resolve()
+    files = folder.rglob("*")
+    for ie in ignore_endswith:
+        files = [ff for ff in files if not ff.name.endswith(ie)]
+    return sorted(files)
+
+
+if __name__ == "__main__":
+    path = pathlib.Path(sys.argv[-1])
+    if not path.is_dir():
+        raise ValueError("Command line argument must be directory!")
+    # output directory
+    pout = path.parent / (path.name + "_tif")
+    pout.mkdir(exist_ok=True)
+    # get input hologram files
+    files = get_paths(path)
+    # conversion
+    for ff in files:
+        # convert image data to uint8 (most image sensors)
+        hol = np.loadtxt(str(ff), dtype=np.uint8)
+        tifout = str(pout / (ff.name[:-10] + ".tif"))
+        # compress image data
+        tifffile.imsave(tifout, hol, compress=9)