Merge branch 'hrixs' into 'master'

hRIXS functions

See merge request !170

src/toolbox_scs/constants.py

@@ -66,6 +66,18 @@ mnemonics = {
     "M2BEND": ({'source': 'SA3_XTD10_MIRR-2/MOTOR/BENDER',
                 'key': 'actualPosition.value',
                 'dim': None},),
+    "hRIXS_det": ({'source': 'SCS_HRIXS_DET/CAM/CAMERA:daqOutput',
+                   'key': 'data.image.pixels',
+                   'dim': ['x', 'y']},),
+    "chem_X": ({'source': 'SCS_CHEM_JET/MOTOR/MANA_X',
+                'key': 'actualPosition.value',
+                'dim': None},),
+    "chem_Y": ({'source': 'SCS_CHEM_JET/MOTOR/MANA_Y',
+                'key': 'actualPosition.value',
+                'dim': None},),
+    "chem_Z": ({'source': 'SCS_CHEM_JET/MOTOR/MANA_Z',
+                'key': 'actualPosition.value',
+                'dim': None},),
     "VSLIT": ({'source': 'SA3_XTD10_VSLIT/MDL/BLADE',
                'key': 'actualGap.value',
                'dim': None},),
@@ -75,6 +87,12 @@ mnemonics = {
     "HSLIT": ({'source': 'SCS_XTD10_HSLIT/MDL/BLADE',
                'key': 'actualGap.value',
                'dim': None},),
+    "H_BLADE_LEFT": ({'source': 'SCS_XTD10_HSLIT/MOTOR/BLADE_LEFT',
+                      'key': 'actualPosition.value',
+                      'dim': None},),
+    "H_BLADE_RIGHT": ({'source': 'SCS_XTD10_HSLIT/MOTOR/BLADE_RIGHT',
+                       'key': 'actualPosition.value',
+                       'dim': None},),
     "transmission": ({'source': 'SA3_XTD10_VAC/MDL/GATT_TRANSMISSION_MONITOR',
                       'key': 'Estimated_Tr.value',
                       'dim': None},

src/toolbox_scs/detectors/__init__.py

@@ -5,6 +5,7 @@ from .dssc import *
 from .dssc_data import *
 from .dssc_misc import *
 from .dssc_processing import *
+from .hrixs import *
 from .pes import *
 from .xgm import *
 
@@ -16,6 +17,7 @@ __all__ = (
     + dssc_data.__all__
     + dssc_misc.__all__
     + dssc_processing.__all__
+    + hrixs.__all__
     + pes.__all__
     + xgm.__all__
 )

src/toolbox_scs/detectors/hrixs.py

+from functools import lru_cache
+
+import numpy as np
+from scipy.optimize import curve_fit
+from scipy.signal import fftconvolve
+
+import toolbox_scs as tb
+
+
+__all__ = [
+    'find_curvature',
+    'correct_curvature',
+    'get_spectrum',
+    'energy_calibration',
+    'calibrate',
+    'gaussian_fit',
+    'to_fwhm'
+]
+
+
+# -----------------------------------------------------------------------------
+# Curvature
+
+def find_curvature(image, frangex=None, frangey=None,
+                   deg=2, axis=1, offset=100):
+    # Resolve arguments
+    x_range = (0, image.shape[1])
+    if frangex is not None:
+        x_range = (max(frangex[0], x_range[0]), min(frangex[1], x_range[1]))
+    y_range = (0, image.shape[0])
+    if frangex is not None:
+        y_range = (max(frangey[0], y_range[0]), min(frangey[1], y_range[1]))
+
+    axis_range = y_range if axis == 1 else x_range
+    axis_dim = image.shape[axis - 1]
+
+    # Get kernel
+    integral = image[slice(*y_range), slice(*x_range)].mean(axis=axis)
+    roi = np.ones([axis_range[1] - axis_range[0], axis_dim])
+    ref = roi * integral[:, np.newaxis]
+
+    # Get sliced image
+    slice_ = [slice(None), slice(None)]
+    slice_[axis - 1] = slice(max(axis_range[0] - offset, 0),
+                             min(axis_range[1] + offset, axis_dim))
+    sliced = image[tuple(slice_)]
+    if axis == 0:
+        sliced = sliced.T
+
+    # Get curvature factor from cross correlation
+    crosscorr = fftconvolve(sliced,
+                            ref[::-1, :],
+                            axes=0, )
+    shifts = np.argmax(crosscorr, axis=0)
+    curv = np.polyfit(np.arange(axis_dim), shifts, deg=deg)
+    return curv[:-1][::-1]
+
+
+def correct_curvature(image, factor=None, axis=1):
+    if factor is None:
+        return
+
+    if axis == 1:
+        image = image.T
+
+    ydim, xdim = image.shape
+    x = np.arange(xdim + 1)
+    y = np.arange(ydim + 1)
+    xx, yy = np.meshgrid(x[:-1] + 0.5, y[:-1] + 0.5)
+    xxn = xx - factor[0] * yy - factor[1] * yy ** 2
+    ret = np.histogramdd((xxn.flatten(), yy.flatten()),
+                         bins=[x, y],
+                         weights=image.flatten())[0]
+
+    return ret if axis == 1 else ret.T
+
+
+def get_spectrum(image, factor=None, axis=0,
+                 pixel_range=None, energy_range=None, ):
+    start, stop = (0, image.shape[axis - 1])
+    if pixel_range is not None:
+        start = max(pixel_range[0] or start, start)
+        stop = min(pixel_range[1] or stop, stop)
+
+    edge = image.sum(axis=axis)[start:stop]
+    bins = np.arange(start, stop + 1)
+    centers = (bins[1:] + bins[:-1]) * 0.5
+    if factor is not None:
+        centers, edge = calibrate(centers, edge,
+                                  factor=factor,
+                                  range_=energy_range)
+
+    return centers, edge
+
+
+# -----------------------------------------------------------------------------
+# Energy calibration
+
+
+def energy_calibration(channels, energies):
+    return np.polyfit(channels, energies, deg=1)
+
+
+def calibrate(x, y=None, factor=None, range_=None):
+    if factor is not None:
+        x = np.polyval(factor, x)
+
+    if y is not None and range_ is not None:
+        start = np.argmin(np.abs((x - range_[0])))
+        stop = np.argmin(np.abs((x - range_[1])))
+        # Calibrated energies have a different direction
+        x, y = x[stop:start], y[stop:start]
+
+    return x, y
+
+
+# -----------------------------------------------------------------------------
+# Gaussian-related functions
+
+
+FWHM_COEFF = 2 * np.sqrt(2 * np.log(2))
+
+
+def gaussian_fit(x_data, y_data, offset=0):
+    """
+    Centre-of-mass and width. Lifted from image_processing.imageCentreofMass()
+    """
+
+    x0 = np.average(x_data, weights=y_data)
+    sx = np.sqrt(np.average((x_data - x0) ** 2, weights=y_data))
+
+    # Gaussian fit
+    baseline = y_data.min()
+    p_0 = (y_data.max(), x0 + offset, sx, baseline)
+    try:
+        p_f, _ = curve_fit(gauss1d, x_data, y_data, p_0, maxfev=10000)
+        return p_f
+    except (RuntimeError, TypeError) as e:
+        print(e)
+        return None
+
+
+def gauss1d(x, height, x0, sigma, offset):
+    return height * np.exp(-0.5 * ((x - x0) / sigma) ** 2) + offset
+
+
+def to_fwhm(sigma):
+    return abs(sigma * FWHM_COEFF)
+
+
+# -----------------------------------------------------------------------------
+# Centroid
+
+THRESHOLD = 510  # pixel counts above which a hit candidate is assumed
+CURVE_A = 2.19042931e-02  # curvature parameters as determined elsewhere
+CURVE_B = -3.02191568e-07
+
+
+def _esrf_centroid(image, threshold=THRESHOLD, curvature=(CURVE_A, CURVE_B)):
+    gs = 2
+    base = image.mean()
+    cp = np.argwhere(image[gs // 2: -gs // 2, gs // 2: -gs // 2] > threshold) + np.array([gs // 2, gs // 2])
+    if len(cp) > 100000:
+        raise RuntimeError('Threshold too low or acquisition time too long')
+
+    res = []
+    for cy, cx in cp:
+        spot = image[cy - gs // 2: cy + gs // 2 + 1, cx - gs // 2: cx + gs // 2 + 1] - base
+        spot[spot < 0] = 0
+        if (spot > image[cy, cx]).sum() == 0:
+            mx = np.average(np.arange(cx - gs // 2, cx + gs // 2 + 1), weights=spot.sum(axis=0))
+            my = np.average(np.arange(cy - gs // 2, cy + gs // 2 + 1), weights=spot.sum(axis=1))
+            my -= (curvature[0] + curvature[1] * mx) * mx
+            res.append((my, mx))
+    return res
+
+
+def _new_centroid(image, threshold=THRESHOLD, curvature=(CURVE_A, CURVE_B)):
+    """find the position of photons with sub-pixel precision
+
+    A photon is supposed to have hit the detector if the intensity within a
+    2-by-2 square exceeds a threshold. In this case the position of the photon
+    is calculated as the center-of-mass in a 4-by-4 square.
+
+    Return the list of x,y coordinate pairs, corrected by the curvature.
+    """
+    base = image.mean()
+    corners = image[1:, 1:] + image[:-1, 1:] + image[1:, :-1] + image[:-1, :-1]
+    threshold = corners.mean() + 3.5 * corners.std()
+    middle = corners[1:-1, 1:-1]
+    candidates = (
+            (middle > threshold)
+            * (middle >= corners[:-2, 1:-1]) * (middle > corners[2:, 1:-1])
+            * (middle >= corners[1:-1, :-2]) * (middle > corners[1:-1, 2:])
+            * (middle >= corners[:-2, :-2]) * (middle > corners[2:, :-2])
+            * (middle >= corners[:-2, 2:]) * (middle > corners[2:, 2:]))
+    cp = np.argwhere(candidates)
+    if len(cp) > 10000:
+        raise RuntimeError(
+            "too many peaks, threshold too low or acquisition time too high")
+
+    res = []
+    for cy, cx in cp:
+        spot = image[cy: cy + 4, cx: cx + 4] - base
+        mx = np.average(np.arange(cx, cx + 4), weights=spot.sum(axis=0))
+        my = np.average(np.arange(cy, cy + 4), weights=spot.sum(axis=1))
+        my -= (curvature[0] + curvature[1] * mx) * mx
+        res.append((my, mx))
+    return res
+
+
+centroid = _new_centroid
+
+
+def decentroid(res):
+    res = np.array(res)
+    ret = np.zeros(shape=(res.max(axis=0) + 1).astype(int))
+    for cy, cx in res:
+        if cx > 0 and cy > 0:
+            ret[int(cy), int(cx)] += 1
+    return ret
+
+
+# -----------------------------------------------------------------------------
+# Integral
+
+FACTOR = 3
+RANGE = [300, 400]
+BINS = abs(np.subtract(*RANGE)) * FACTOR
+
+
+def parabola(x, a, b, c=0):
+    return (a * x + b) * x + c
+
+
+def integrate(image, factor=FACTOR, range=RANGE, curvature=(CURVE_A, CURVE_B), ):
+    image = image - image.mean()
+    x = np.arange(image.shape[1])[None, :]
+    y = np.arange(image.shape[0])[:, None]
+    ys = factor * (y - parabola(x, curvature[1], curvature[0]))
+    ysf = np.floor(ys)
+    rang = (factor * range[0], factor * range[1])
+    bins = rang[1] - rang[0]
+    lhy, lhx = np.histogram(ysf.ravel(), bins=bins, weights=((ys - ysf) * image).ravel(), range=rang)
+    rhy, rhx = np.histogram((ysf + 1).ravel(), bins=bins, weights=(((ysf + 1) - ys) * image).ravel(), range=rang)
+    lvy, lvx = np.histogram(ysf.ravel(), bins=bins, weights=(ys - ysf).ravel(), range=rang)
+    rvy, rvx = np.histogram((ysf + 1).ravel(), bins=bins, weights=((ysf + 1) - ys).ravel(), range=rang)
+    return (lhy + rhy) / (lvy + rvy)
+
+
+# -----------------------------------------------------------------------------
+# hRIXS class
+
+
+class hRIXS:
+    # run
+    PROPOSAL = 2769
+
+    # image range
+    X_RANGE = np.s_[1300:-100]
+    Y_RANGE = np.s_[:]
+
+    # centroid
+    THRESHOLD = THRESHOLD  # pixel counts above which a hit candidate is assumed
+    CURVE_A = CURVE_A  # curvature parameters as determined elsewhere
+    CURVE_B = CURVE_B
+
+    # integral
+    FACTOR = FACTOR
+    RANGE = RANGE
+    BINS = abs(np.subtract(*RANGE)) * FACTOR
+
+    METHOD = 'centroid'  # ['centroid', 'integral']
+
+    @classmethod
+    def set_params(cls, **params):
+        for key, value in params.items():
+            setattr(cls, key.upper(), value)
+
+    def __set_params(self, **params):
+        self.__class__.set_params(**params)
+        self.refresh()
+
+    @classmethod
+    def get_params(cls, *params):
+        if not params:
+            params = ('proposal', 'x_range', 'y_range',
+                      'threshold', 'curve_a', 'curve_b',
+                      'factor', 'range', 'bins',
+                      'method')
+        return {param: getattr(cls, param.upper()) for param in params}
+
+    def refresh(self):
+        cls = self.__class__
+        for cached in ['_centroid', '_integral']:
+            getattr(cls, cached).fget.cache_clear()
+
+    def __init__(self, images, norm=None):
+        self.images = images
+        self.norm = norm
+
+        # class/instance method compatibility
+        self.set_params = self.__set_params
+
+    @classmethod
+    def from_run(cls, runNB, proposal=None, first_wrong=False):
+        if proposal is None:
+            proposal = cls.PROPOSAL
+
+        run, data = tb.load(proposal, runNB=runNB, fields=['hRIXS_det'])
+
+        # Get slow train data
+        mnemo = tb.mnemonics_for_run(run)['SCS_slowTrain']
+        slow_train = run[mnemo['source'], mnemo['key']].ndarray().sum()
+
+        return cls(images=data['hRIXS_det'][1 if first_wrong else 0:].data,
+                   norm=slow_train)
+
+    @property
+    @lru_cache()
+    def _centroid(self):
+        return sum((centroid(image[self.Y_RANGE, self.X_RANGE].T,
+                             threshold=self.THRESHOLD,
+                             curvature=(self.CURVE_A, self.CURVE_B), )
+                    for image in self.images), [])
+
+    def _centroid_spectrum(self, bins=None, range=None, normalize=True):
+        if bins is None:
+            bins = self.BINS
+        if range is None:
+            range = self.RANGE
+
+        r = np.array(self._centroid)
+        hy, hx = np.histogram(r[:, 0], bins=bins, range=range)
+        if normalize and self.norm is not None:
+            hy = hy / self.norm
+
+        return (hx[:-1] + hx[1:]) / 2, hy
+
+    @property
+    @lru_cache()
+    def _integral(self):
+        return sum((integrate(image[self.Y_RANGE, self.X_RANGE].T,
+                              factor=self.FACTOR,
+                              range=self.RANGE,
+                              curvature=(self.CURVE_A, self.CURVE_B))
+                    for image in self.images))
+
+    def _integral_spectrum(self, normalize=True):
+        values = self._integral
+        if normalize and self.norm is not None:
+            values = values / self.norm
+        return np.arange(values.size), values
+
+    @property
+    def corrected(self):
+        return decentroid(self._centroid)
+
+    def spectrum(self, normalize=True):
+        spec_func = (self._centroid_spectrum if self.METHOD.lower() == 'centroid'
+                     else self._integral_spectrum)
+        return spec_func(normalize=normalize)
+
+    def __sub__(self, other):
+        px, py = self.spectrum()
+        mx, my = other.spectrum()
+        return (px + mx) / 2, py - my
+
+    def __add__(self, other):
+        return self.__class__(images=list(self.images) + list(other.images),
+                              norm=self.norm + other.norm)