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csst_mci_sim/support/cosmicrays.py

+"""
+Cosmic Rays
+===========
+
+This simple class can be used to include cosmic ray events to an image.
+By default the cosmic ray events are drawn from distributions describing
+the length and energy of the events. Such distributions can be generated
+for example using Stardust code (http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=04636917).
+The energy of the cosmic ray events can also be set to constant for
+testing purposes. The class can be used to draw a single cosmic ray
+event or up to a covering fraction.
+
+:requires: NumPy
+:requires: SciPy
+
+:version: 0.2
+
+"""
+import numpy as np
+from scipy.interpolate import InterpolatedUnivariateSpline
+
+
+class cosmicrays():
+    """
+    Cosmic ray generation class. Can either draw events from distributions or
+    set the energy of the events to a constant.
+
+    :param log: logger instance
+    :param image: image to which cosmic rays are added to (a copy is made not to change the original numpy array)
+    :param crInfo: column information (cosmic ray file)
+    :param information: cosmic ray track information (file containing track length and energy information) and
+                        exposure time.
+    """
+
+    def __init__(self, log, image, exptime, crInfo=None, information=None):
+        """
+        Cosmic ray generation class. Can either draw events from distributions or
+        set the energy of the events to a constant.
+
+        :param log: logger instance
+        :param image: image to which cosmic rays are added to (a copy is made not to change the original numpy array)
+        :param crInfo: column information (cosmic ray file)
+        :param information: cosmic ray track information (file containing track length and energy information) and
+                            exposure time.
+        """
+
+        self.exptime = exptime
+
+        self.log = log
+
+        #image and size
+        self.image = image.copy()
+        self.ysize, self.xsize = self.image.shape
+
+        if crInfo is not None:
+            self.cr = crInfo
+        else:
+            self._readCosmicrayInformation()
+
+
+##################################################
+
+
+    def _cosmicRayIntercepts(self, lum, x0, y0, l, phi):
+        """
+        Derive cosmic ray streak intercept points.
+
+        :param lum: luminosities of the cosmic ray tracks
+        :param x0: central positions of the cosmic ray tracks in x-direction
+        :param y0: central positions of the cosmic ray tracks in y-direction
+        :param l: lengths of the cosmic ray tracks
+        :param phi: orientation angles of the cosmic ray tracks
+
+        :return: cosmic ray map (image)
+        :rtype: nd-array
+        """
+        # create empty array
+        crImage = np.zeros((self.ysize, self.xsize), dtype=np.float64)
+
+        # x and y shifts
+        dx = l * np.cos(phi) / 2.
+        dy = l * np.sin(phi) / 2.
+        mskdx = np.abs(dx) < 1e-8
+        mskdy = np.abs(dy) < 1e-8
+        dx[mskdx] = 0.
+        dy[mskdy] = 0.
+
+        #pixels in x-direction
+        ilo = np.round(x0.copy() - dx)
+        msk = ilo < 0.
+        ilo[msk] = 0
+        ilo = ilo.astype(int)
+
+        ihi = 1 + np.round(x0.copy() + dx)
+        msk = ihi > self.xsize
+        ihi[msk] = self.xsize
+        ihi = ihi.astype(int)
+
+        #pixels in y-directions
+        jlo = np.round(y0.copy() - dy)
+        msk = jlo < 0.
+        jlo[msk] = 0
+        jlo = jlo.astype(int)
+
+        jhi = 1 + np.round(y0.copy() + dy)
+        msk = jhi > self.ysize
+        jhi[msk] = self.ysize
+        jhi = jhi.astype(int)
+
+        # loop over the individual events
+        for i, luminosity in enumerate(lum):
+            n = 0  # count the intercepts
+
+            u = []
+            x = []
+            y = []
+
+            # Compute X intercepts on the pixel grid
+            if ilo[i] < ihi[i]:
+                for xcoord in range(ilo[i], ihi[i]):
+                    ok = (xcoord - x0[i]) / dx[i]
+                    if np.abs(ok) <= 0.5:
+                        n += 1
+                        u.append(ok)
+                        x.append(xcoord)
+                        y.append(y0[i] + ok * dy[i])
+            else:
+                for xcoord in range(ihi[i], ilo[i]):
+                    ok = (xcoord - x0[i]) / dx[i]
+                    if np.abs(ok) <= 0.5:
+                        n += 1
+                        u.append(ok)
+                        x.append(xcoord)
+                        y.append(y0[i] + ok * dy[i])
+
+            # Compute Y intercepts on the pixel grid
+            if jlo[i] < jhi[i]:
+                for ycoord in range(jlo[i], jhi[i]):
+                    ok = (ycoord - y0[i]) / dy[i]
+                    if np.abs(ok) <= 0.5:
+                        n += 1
+                        u.append(ok)
+                        x.append(x0[i] + ok * dx[i])
+                        y.append(ycoord)
+            else:
+                for ycoord in range(jhi[i], jlo[i]):
+                    ok = (ycoord - y0[i]) / dy[i]
+                    if np.abs(ok) <= 0.5:
+                        n += 1
+                        u.append(ok)
+                        x.append(x0[i] + ok * dx[i])
+                        y.append(ycoord)
+
+            # check if no intercepts were found
+            if n < 1:
+                xc = int(np.floor(x0[i]))
+                yc = int(np.floor(y0[i]))
+                crImage[yc, xc] += luminosity
+
+            # Find the arguments that sort the intersections along the track
+            u = np.asarray(u)
+            x = np.asarray(x)
+            y = np.asarray(y)
+
+            args = np.argsort(u)
+
+            u = u[args]
+            x = x[args]
+            y = y[args]
+
+            # Decide which cell each interval traverses, and the path length
+            for i in range(1, n - 1):
+                w = u[i + 1] - u[i]
+                cx = int(1 + np.floor((x[i + 1] + x[i]) / 2.))
+                cy = int(1 + np.floor((y[i + 1] + y[i]) / 2.))
+
+                if 0 <= cx < self.xsize and 0 <= cy < self.ysize:
+                    crImage[cy, cx] += (w * luminosity)
+
+        return crImage
+
+
+############################################################################
+
+
+    def _drawEventsToCoveringFactor(self, coveringFraction=3.0, limit=1000, verbose=False):
+        """
+        Generate cosmic ray events up to a covering fraction and include it to a cosmic ray map (self.cosmicrayMap).
+
+        :param coveringFraction: covering fraction of cosmic rya events in per cent of total number of pixels
+        :type coveringFraction: float
+        :param limit: limiting energy for the cosmic ray event [None = draw from distribution]
+        :type limit: None or float
+        :param verbose: print out information to stdout
+        :type verbose: bool
+
+
+        :return: None
+        """
+        self.cosmicrayMap = np.zeros((self.ysize, self.xsize))
+
+        # how many events to draw at once, too large number leads to exceeding the covering fraction
+        ####cr_n = int(295 * self.exptime / 565. * coveringFraction / 1.4)
+
+        cr_n = int(5000 * self.exptime / 565. * coveringFraction)
+
+        covering = 0.0
+
+        while covering < coveringFraction:
+            # pseudo-random numbers taken from a uniform distribution between 0 and 1
+            np.random.seed()
+            luck = np.random.rand(cr_n)
+
+            # draw the length of the tracks
+            ius = InterpolatedUnivariateSpline(
+                self.cr['cr_cdf'], self.cr['cr_u'])
+            self.cr['cr_l'] = ius(luck)
+
+            if limit is None:
+                ius = InterpolatedUnivariateSpline(
+                    self.cr['cr_cde'], self.cr['cr_v'])
+                self.cr['cr_e'] = ius(luck)
+            else:
+                # set the energy directly to the limit
+                self.cr['cr_e'] = np.asarray([limit,])
+
+            # Choose the properties such as positions and an angle from a random Uniform dist
+            np.random.seed()
+            cr_x = self.xsize * np.random.rand(int(np.floor(cr_n)))
+
+            np.random.seed()
+            cr_y = self.ysize * np.random.rand(int(np.floor(cr_n)))
+
+            np.random.seed()
+            cr_phi = np.pi * np.random.rand(int(np.floor(cr_n)))
+
+            # find the intercepts
+            self.cosmicrayMap += self._cosmicRayIntercepts(
+                self.cr['cr_e'], cr_x, cr_y, self.cr['cr_l'], cr_phi)
+
+            # count the covering factor
+            area_cr = np.count_nonzero(self.cosmicrayMap)
+            covering = 100.*area_cr / (self.xsize*self.ysize)
+
+            text = 'The cosmic ray covering factor is %i pixels i.e. %.3f per cent' % (
+                area_cr, covering)
+            self.log.info(text)
+
+# 33
+
+    def addUpToFraction(self, coveringFraction, limit=None, verbose=False):
+        """
+        Add cosmic ray events up to the covering Fraction.
+
+        :param coveringFraction: covering fraction of cosmic rya events in per cent of total number of pixels
+        :type coveringFraction: float
+        :param limit: limiting energy for the cosmic ray event [None = draw from distribution]
+        :type limit: None or float
+        :param verbose: print out information to stdout
+        :type verbose: bool
+
+        :return: image with cosmic rays
+        :rtype: ndarray
+        """
+        self._drawEventsToCoveringFactor(
+            coveringFraction, limit=limit, verbose=verbose)
+
+        # paste cosmic rays
+        self.image += self.cosmicrayMap
+
+        return self.image