initial commit of likelihood fit for muons

This commit contains code to fit for the energy, position, and direction of
muons in the SNO detector. Currently, we read events from SNOMAN zebra files
and fill an event struct containing the PMT hits and fit it with the Nelder
Mead simplex algorithm from GSL.

I've also added code to read in ZEBRA title bank files to read in the DQXX
files for a specific run. Any problems with channels in the DQCH and DQCR banks
are flagged in the event struct by masking in a bit in the flags variable and
these PMT hits are not included in the likelihood calculation.

The likelihood for an event is calculated by integrating along the particle
track for each PMT and computing the expected number of PE. The charge
likelihood is then calculated by looping over all possible number of PE and
computing:

    P(q|n)*P(n|mu)

where q is the calibrated QHS charge, n is the number of PE, and mu is the
expected number of photoelectrons. The latter is calculated assuming the
distribution of PE at a given PMT follows a Poisson distribution (which I think
should be correct given the track, but is probably not perfect for tracks which
scatter a lot).

The time part of the likelihood is calculated by integrating over the track for
each PMT and calculating the average time at which the PMT is hit. We then
assume the PDF for the photons to arrive is approximately a delta function and
compute the first order statistic for a given time to compute the probability
that the first photon arrived at a given time. So far I've only tested this
with single tracks but the method was designed to be easy to use when you are
fitting for multiple particles.

1 files changed, 219 insertions, 0 deletions

diff --git a/zebra.c b/zebra.c
new file mode 100644
index 0000000..4ce51a2
--- /dev/null
+++ b/zebra.c
@@ -0,0 +1,219 @@
+#include "zebra.h"
+#include <stdio.h> /* for FILE */
+#include <stdlib.h> /* for size_t */
+#include "pack2b.h"
+#include <string.h> /* for memmove() */
+#include <stdint.h> /* for uint8_t, etc. */
+#include <errno.h> /* for strerror(), etc. */
+
+char zebra_err[256];
+
+zebraFile *zebra_open(const char *filename)
+{
+    FILE *f = fopen(filename, "r");
+
+    if (!f) {
+        sprintf(zebra_err, "failed to open '%s': %s", filename, strerror(errno));
+        return NULL;
+    }
+
+    zebraFile *z = (zebraFile *) malloc(sizeof(zebraFile));
+    z->f = f;
+    z->offset = 0;
+    z->lr_size = 0;
+    z->buf = NULL;
+    z->buf_size = 0;
+
+    return z;
+}
+
+int read_next_physical_record(zebraFile *z)
+{
+    /* Read the next physical record from the zebra file and append it to the
+     * buffer.
+     *
+     * Returns 0 on success, -1 on error, and 1 on EOF. */
+    uint8_t buf[48];
+    size_t nbytes;
+    uint32_t s0, s1, s2, s3, nwphr, nfast;
+
+    nbytes = fread(buf,4,8,z->f);
+
+    if (nbytes == 0) return 1;
+
+    if (nbytes != 8) {
+        sprintf(zebra_err, "expected %i words but only read %zu", 8, nbytes);
+        return -1;
+    }
+
+    s0 = unpacki32(buf);
+    s1 = unpacki32(buf+4*1);
+    s2 = unpacki32(buf+4*2);
+    s3 = unpacki32(buf+4*3);
+    nwphr = unpacki32(buf+4*4);
+    nfast = unpacki32(buf+7*4);
+
+    if (nwphr & (ZEBRA_EMERGENCY_STOP | ZEBRA_END_OF_RUN))
+        return 1;
+
+    nwphr &= ZEBRA_BLOCK_SIZE_MASK;
+
+    uint32_t words = nwphr*(1 + nfast) - 8;
+
+    if (s0 != ZEBRA_SIG0) {
+        sprintf(zebra_err, "invalid steering block stamp 0x%08x", s0);
+        return -1;
+    }
+
+    if (s1 != ZEBRA_SIG1) {
+        sprintf(zebra_err, "invalid steering block stamp 0x%08x", s1);
+        return -1;
+    }
+
+    if (s2 != ZEBRA_SIG2) {
+        sprintf(zebra_err, "invalid steering block stamp 0x%08x", s2);
+        return -1;
+    }
+
+    if (s3 != ZEBRA_SIG3) {
+        sprintf(zebra_err, "invalid steering block stamp 0x%08x", s3);
+        return -1;
+    }
+
+    z->buf = realloc(z->buf, z->buf_size+words*4);
+
+    nbytes = fread(z->buf+z->buf_size, 4, words, z->f);
+
+    z->buf_size += words*4;
+
+    if (nbytes != words) {
+        sprintf(zebra_err, "expected %i words but only read %zu", words, nbytes);
+        return -1;
+    }
+
+    return 0;
+}
+
+int get_bytes(zebraFile *z, size_t size)
+{
+    /* Read bytes from the zdab file until there are at least `size` words in
+     * the buffer.
+     *
+     * Returns 0 on success, -1 on error, and 1 on EOF. */
+    int rv;
+
+    while ((z->buf_size - z->offset) < size*4) {
+        rv = read_next_physical_record(z);
+
+        if (rv == -1) {
+            return -1;
+        } else if (z->buf_size == 0 && rv == 1) {
+            /* EOF and there are no bytes left. */
+            return 1;
+        }
+    }
+
+    return 0;
+}
+
+int read_next_logical_record(zebraFile *z)
+{
+    /* Read the next logical record into the buffer.
+     *
+     * Returns 0 on success, -1 on error, and 1 on EOF. */
+    uint32_t size, type, nwtx, nwseg, nwtab, nwuh;
+
+    while (1) {
+        memmove(z->buf,z->buf+z->offset,z->buf_size-z->offset);
+        z->buf = realloc(z->buf, z->buf_size-z->offset);
+        z->buf_size -= z->offset;
+        z->offset = 0;
+
+        switch (get_bytes(z,1)) {
+        case 1:
+            return 1;
+        case -1:
+            return -1;
+        }
+        size = unpacki32(z->buf+z->offset);
+        z->offset += 4;
+
+        if (size == 0) continue;
+
+        switch (get_bytes(z,1)) {
+        case 1:
+            return 1;
+        case -1:
+            return -1;
+        }
+        type = unpacki32(z->buf+z->offset);
+        z->offset += 4;
+
+        switch (type) {
+        case 5:
+        case 6:
+            get_bytes(z,size-1);
+            z->offset += (size-1)*4;
+            continue;
+        case 1:
+            get_bytes(z,size);
+            z->offset += size*4;
+            continue;
+        }
+
+        z->lr_size = (size + 2)*4;
+        get_bytes(z,size);
+
+        nwtx = unpacki32(z->buf+z->offset+4*4);
+        nwseg = unpacki32(z->buf+z->offset+5*4);
+        nwtab = unpacki32(z->buf+z->offset+6*4);
+        nwuh = unpacki32(z->buf+z->offset+9*4);
+
+        z->offset += 10*4;
+
+        z->offset += nwtx*4;
+        z->offset += nwseg*4;
+        z->offset += nwtab*4;
+        z->offset += nwuh*4;
+
+        break;
+    }
+
+    return 0;
+}
+
+int next_bank(zebraFile *z, bank *b)
+{
+    int rv;
+    uint32_t io, noff;
+
+    if (z->offset == z->lr_size) {
+        rv = read_next_logical_record(z);
+        if (rv) return rv;
+    }
+
+    io = unpacki32(z->buf+z->offset);
+    z->offset += 4;
+
+    noff = io & 0xFFFF;
+
+    if (noff > 12) {
+        z->offset += (noff-12)*4;
+    }
+
+    unpack(z->buf+z->offset,"lllllllll",&b->next, &b->up, &b->orig, &b->number, &b->name, &b->num_links, &b->num_structural_links, &b->num_data_words, &b->status);
+    z->offset += 9*4;
+
+    b->data = (uint32_t *) (z->buf+z->offset);
+
+    z->offset += b->num_data_words*4;
+
+    return 0;
+}
+
+void zebra_close(zebraFile *z)
+{
+    fclose(z->f);
+    if (z->buf) free(z->buf);
+    free(z);
+}