From 23fde89b681c07e67ae52783ab8361ac98d24f53 Mon Sep 17 00:00:00 2001
From: Michael Schneider <mschneid@mbi-berlin.de>
Date: Mon, 5 Oct 2020 18:24:37 +0200
Subject: [PATCH] azimuthal integrator using DSSC geometry object
---
src/toolbox_scs/detectors/__init__.py | 3 +-
.../detectors/azimuthal_integrator.py | 99 ++++++++++++++++++-
src/toolbox_scs/detectors/dssc_misc.py | 4 +-
3 files changed, 102 insertions(+), 4 deletions(-)
diff --git a/src/toolbox_scs/detectors/__init__.py b/src/toolbox_scs/detectors/__init__.py
index 5059545..ae6fe76 100644
--- a/src/toolbox_scs/detectors/__init__.py
+++ b/src/toolbox_scs/detectors/__init__.py
@@ -11,7 +11,7 @@ from .dssc_processing import (
bin_data)
from .dssc import (
DSSCBinner, DSSCFormatter, DSSCAnalyzer)
-from .azimuthal_integrator import AzimuthalIntegrator
+from .azimuthal_integrator import AzimuthalIntegrator, AzimuthalIntegratorDSSC
__all__ = (
# Functions
@@ -35,6 +35,7 @@ __all__ = (
"DSSCFormatter",
"DSSCAnalyzer",
"AzimuthalIntegrator",
+ "AzimuthalIntegratorDSSC",
# Variables
)
diff --git a/src/toolbox_scs/detectors/azimuthal_integrator.py b/src/toolbox_scs/detectors/azimuthal_integrator.py
index fb56490..dd50c70 100644
--- a/src/toolbox_scs/detectors/azimuthal_integrator.py
+++ b/src/toolbox_scs/detectors/azimuthal_integrator.py
@@ -78,6 +78,103 @@ class AzimuthalIntegrator(object):
def __call__(self, image):
assert self.shape == image.shape, 'image shape does not match'
- image_flat = image.flatten()
+ image_flat = np.ravel(image)
return np.array([np.nansum(image_flat[indices]) \
for indices in self.flat_indices])
+
+
+class AzimuthalIntegratorDSSC(object):
+ def __init__(self, geom, polar_range, nrings=100, dxdy=(0, 0)):
+ '''
+ Create a reusable integrator for repeated azimuthal integration of
+ similar images. Calculates array indices for a given parameter set that
+ allows fast recalculation. Directly uses a extra_geom.detectors.DSSC_1MGeometry
+ instance for correct pixel positions
+
+ Parameters
+ ==========
+ geom : extra_geom.detectors.DSSC_1MGeometry
+ loaded geometry instance
+
+ polar_range : tuple of ints
+ start and stop polar angle (in degrees) to restrict integration to
+ wedges
+
+ nrings : int, default 100
+ number of rings to integrate over
+
+ dxdy : tuple of floats, default (0, 0)
+ global coordinate shift to adjust center outside of geom object
+
+ 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
+ '''
+ pos = geom.get_pixel_positions()
+ self.shape = pos.shape[:-1]
+ xcoord, ycoord = pos[..., 0] + dxdy[0], pos[..., 1] + dxdy[1]
+
+ # distance from center
+ dist_array = np.hypot(xcoord, ycoord)
+
+ # array of polar angles
+ if np.abs(polar_range[1] - polar_range[0]) > 180:
+ raise ValueError('Integration angle too wide, should be within 180'
+ ' degrees')
+
+ if np.abs(polar_range[1] - polar_range[0]) < 1e-6:
+ raise ValueError('Integration angle too narrow')
+
+ if np.abs(polar_range[1] - polar_range[0]) == 180:
+ self.polar_mask = np.ones_like(pos)
+ else:
+ 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)
+
+ maxdist = np.abs(dist_array).max()
+ dr = maxdist / nrings
+
+ im, ix, iy = np.indices(dimensions=self.shape)
+ self.index_array = np.ravel_multi_index((im, ix, iy), self.shape)
+
+ self.distance = []
+ self.flat_indices = []
+ for dist in np.arange(dr, 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.append(dist)
+ self.distance = np.array(self.distance)
+
+ def calc_q(self, distance, wavelength):
+ '''Calculate momentum transfer coordinate.
+
+ Parameters
+ ==========
+ distance : float
+ Sample - detector distance in meter
+ wavelength : float
+ wavelength of scattered light in meters
+
+ Returns
+ =======
+ deltaq : np.ndarray
+ Momentum transfer coordinate for azimuthal integration
+ '''
+ return 4 * np.pi * np.sin(np.arctan(self.distance / distance)) / wavelength
+
+ def __call__(self, image):
+ assert self.shape == image.shape, 'image shape does not match'
+ image_flat = np.ravel(image)
+ return np.array([np.nansum(image_flat[indices])
+ for indices in self.flat_indices])
\ No newline at end of file
diff --git a/src/toolbox_scs/detectors/dssc_misc.py b/src/toolbox_scs/detectors/dssc_misc.py
index 5f9a2f6..d7a2202 100644
--- a/src/toolbox_scs/detectors/dssc_misc.py
+++ b/src/toolbox_scs/detectors/dssc_misc.py
@@ -178,7 +178,7 @@ def load_geom(geopath=None, quad_pos=None):
return geom
-def quickmask_DSSC_ASIC(geom, poslist):
+def quickmask_DSSC_ASIC(poslist):
'''
Returns a mask for the given DSSC geometry with ASICs given in poslist
blanked. poslist is a list of (module, row, column) tuples. Each module
@@ -192,7 +192,7 @@ def quickmask_DSSC_ASIC(geom, poslist):
for (module, row, col) in poslist:
mask[module, 64 * row:64 * (row + 1), 64 * col:64 * (col + 1)] = \
np.nan
- return geom.position_modules_fast(mask)[0]
+ return mask
def load_mask(fname, dssc_mask):
--
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