docs: add example

Author: paulmueller

CHANGELOG

@@ -1,7 +1,7 @@
 0.3.0
  - ref: renamed `meta.DATA_KEYS` to `meta.DATA_KEYS_FL` and removed
    keys that are not relevant for fluorescence imaging
- - docs: initial documentation with code reference
+ - docs: initial documentation with code reference and example
 0.2.1
  - maintenance release
 0.2.0

docs/sec_examples.rst

@@ -6,3 +6,4 @@ Examples
   :maxdepth: 2
 
 
+.. fancy_include:: simple_fluorescence.py

examples/data/retina_p10.h5

@@ -0,0 +1,33 @@
+import os
+import os.path as op
+import sys
+
+import matplotlib.pylab as plt
+
+thisdir = op.dirname(op.abspath(__file__))
+sys.path.insert(0, op.dirname(thisdir))
+
+DPI = 80
+
+
+if __name__ == "__main__":
+    # Do not display example plots
+    plt.show = lambda: None
+    files = os.listdir(thisdir)
+    files = [f for f in files if f.endswith(".py")]
+    files = [f for f in files if not f == op.basename(__file__)]
+    files = sorted([op.join(thisdir, f) for f in files])
+
+    for f in files:
+        fname = f[:-3] + ".jpg"
+        if not op.exists(fname):
+            exec_str = open(f).read()
+            if exec_str.count("plt.show()"):
+                exec(exec_str)
+                plt.savefig(fname, dpi=DPI)
+                print("Image created: '{}'".format(fname))
+            else:
+                print("No image: '{}'".format(fname))
+        else:
+            print("Image skipped (already exists): '{}'".format(fname))
+        plt.close()

examples/generate_example_images.py

@@ -0,0 +1,27 @@
+"""Loading and plotting
+
+This example illustrates the simple usage of the
+:class:`flimage.FLImage <flimage.core.FLImage>` class for reading and
+managing quantitative phase data. The attribute ``FLImage.fluorescence``
+yields the image data.
+
+The image shows a young retina cell. The original dataset, available on
+`figshare <https://doi.org/10.6084/m9.figshare.8055407.v1>`_
+(*retina-young_sinogram_fli.h5*) :cite:`Schuermann2017`, can be opened in
+the same manner using the
+:class:`flimage.FLSeries <flimage.series.FLSeries>` class.
+"""
+import matplotlib.pylab as plt
+import flimage
+
+# load the experimental data
+fli = flimage.FLImage(h5file="./data/retina_p10.h5", h5mode="r")
+
+# plot
+plt.figure(figsize=(4, 3))
+
+plt.subplot(title="fluorescence image of a mouse retina cell")
+plt.imshow(fli.fl, cmap="YlGnBu_r")
+
+plt.tight_layout()
+plt.show()