Merge pull request #7 from LaurentRDC/4.0

4 0

iris/__init__.py

@@ -1,7 +1,8 @@
 # -*- coding: utf-8 -*-
 
+from .beam_properties import beam_properties
 from .dataset import DiffractionDataset, PowderDiffractionDataset
 from .knife_edge import cdf, knife_edge
 from .optimizations import cached_property
+from .raw import parse_tagfile, RawDataset
 from .utils import scattering_length
-from .raw import RawDataset

iris/beam_properties.py

@@ -0,0 +1,65 @@
+
+import numpy as np
+from skimage.io import imread
+from os.path import join
+from glob import glob
+from warnings import warn
+
+from .raw import parse_tagfile
+
+# TODO: beam pointing stability using scikit-image's register_translation?
+
+def beam_properties(directory, reprate = 1000, exposure = None, energy = None, callback = None):
+    """ 
+    Calculates electron beam properties from a ponderomotive-style
+    measurement. Properties monitored are average electron count per shot and
+    electron count stability.
+
+    Parameters
+    ----------
+    directory : str or path-like object
+        Absolute path to the directory
+    reprate : int, optional
+        Laser repetition rate [Hz]. Default is 1000.
+    exposure : float, optional
+        Exposure time [s]. If None (default), the value will be inferred from
+        `directory/tagfile.txt`
+    energy : float, optional
+        Electron energy [keV]. If None (default), the value will be inferred from
+        `directory/tagfile.txt`.
+    callback : callable or None, optional
+        Callable of a single argument, to which the calculation progress will be passed as
+        an integer between 0 and 100.
+    
+    Returns
+    -------
+    properties : dict
+        Dictionary with keys 'count' and 'stability'. The value for the 'count' key is
+        the average number of electron per shot. The value for the 'stability' key is the
+        standard deviation (in percent of the average) in the 'count' value.
+    """
+    if callback is None:
+        callback = lambda _: None
+
+    metadata = parse_tagfile(join(directory, 'tagfile.txt'))
+    exposure = metadata['exposure']
+    energy = metadata['energy'] or 90
+
+    # Conversion between pixel intensity and number of electrons
+    # depends on electron energy
+    # Conversion taken from lowECount.m
+    conv = 0.1862*energy - 0.5660
+    n_pulses = exposure*reprate
+
+    bg_filenames = glob(join(directory, 'background*.tif'))
+    background = sum(imread(path).astype(np.float) for path in bg_filenames)/len(bg_filenames)
+
+    images = glob(join(directory, 'data.timedelay.*.pumpon.tif'))
+    e_count = list()
+    for i, fn in enumerate(images):
+        im = (imread(fn).astype(np.float) - background).clip(min = 0)
+        e_count.append(np.sum(im)/conv/n_pulses)
+        callback(int(100*i/len(images)))
+
+    return {'count': np.mean(e_count), 
+            'stability': np.std(e_count)/np.mean(e_count) * 100}