Merge branch 'crunchDSSC' into 'master'

DSSC multiprocessing analysis

See merge request !45

__init__.py

@@ -3,3 +3,5 @@ from ToolBox.xgm import *
 from ToolBox.XAS import *
 from ToolBox.knife_edge import *
 from ToolBox.Laser_utils import *
+from ToolBox.DSSC import DSSC
+from ToolBox.azimuthal_integrator import *

azimuthal_integrator.py

+import numpy as np
+
+class azimuthal_integrator(object):
+    def __init__(self, imageshape, center, polar_range, dr=2):
+        '''
+        Create a reusable integrator for repeated azimuthal integration of similar
+        images. Calculates array indices for a given parameter set that allows
+        fast recalculation.
+        
+        Parameters
+        ==========
+        imageshape : tuple of ints
+            The shape of the images to be integrated over.
+            
+        center : tuple of ints
+            center coordinates in pixels
+        
+        polar_range : tuple of ints
+            start and stop polar angle (in degrees) to restrict integration to wedges
+        
+        dr : int, default 2
+            radial width of the integration slices. Takes non-square DSSC pixels into account.
+        
+        Returns
+        =======
+        ai : azimuthal_integrator instance
+            Instance can directly be called with image data:
+            > az_intensity = ai(image)
+            radial distances and the polar mask are accessible as attributes:
+            > ai.distance
+            > ai.polar_mask
+        '''
+        self.shape = imageshape
+        cx, cy = center
+        sx, sy = imageshape
+        xcoord, ycoord = np.ogrid[:sx, :sy]
+        xcoord -= cx
+        ycoord -= cy
+
+        # distance from center, hexagonal pixel shape taken into account
+        dist_array = np.hypot(xcoord * 204 / 236, ycoord)
+
+        # array of polar angles
+        tmin, tmax = np.deg2rad(np.sort(polar_range)) % np.pi
+        polar_array = np.arctan2(xcoord, ycoord)
+        polar_array = np.mod(polar_array, np.pi)
+        self.polar_mask = (polar_array > tmin) * (polar_array < tmax)
+
+        self.maxdist = min(sx  - cx, sy  - cy)
+
+        ix, iy = np.indices(dimensions=(sx, sy))
+        self.index_array = np.ravel_multi_index((ix, iy), (sx, sy))
+
+        self.distance = np.array([])
+        self.flat_indices = []
+        for dist in range(dr, self.maxdist, dr):
+            ring_mask = self.polar_mask * (dist_array >= (dist - dr)) * (dist_array < dist)
+            self.flat_indices.append(self.index_array[ring_mask])
+            self.distance = np.append(self.distance, dist)
+    
+    def __call__(self, image):
+        assert self.shape == image.shape, 'image shape does not match'
+        image_flat = image.flatten()
+        return np.array([np.nansum(image_flat[indices]) for indices in self.flat_indices])