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, 48 insertions, 0 deletions

diff --git a/zebra.h b/zebra.h
new file mode 100644
index 0000000..2f24939
--- /dev/null
+++ b/zebra.h
@@ -0,0 +1,48 @@
+#ifndef ZEBRA_H
+#define ZEBRA_H
+
+#include <stdio.h> /* for FILE */
+#include <stdlib.h> /* for size_t */
+#include <stdint.h> /* for uint8_t, etc. */
+
+extern char zebra_err[256];
+
+#define ZEBRA_SIG0 0x0123cdefUL
+#define ZEBRA_SIG1 0x80708070UL
+#define ZEBRA_SIG2 0x4321abcdUL
+#define ZEBRA_SIG3 0x80618061UL
+
+#define ZEBRA_BLOCK_SIZE_MASK 0x00ffffffUL
+#define ZEBRA_EMERGENCY_STOP  0x80000000UL
+#define ZEBRA_END_OF_RUN      0x20000000UL
+#define ZEBRA_START_OF_RUN    0x40000000UL
+
+typedef struct bank {
+    uint32_t next;
+    uint32_t up;
+    uint32_t orig;
+    uint32_t number;
+    uint32_t name;
+    uint32_t num_links;
+    uint32_t num_structural_links;
+    uint32_t num_data_words;
+    uint32_t status;
+    uint32_t *data;
+} bank;
+
+typedef struct zebraFile {
+    FILE *f;
+    size_t offset;
+    size_t lr_size;
+    uint8_t *buf;
+    size_t buf_size;
+} zebraFile;
+
+zebraFile *zebra_open(const char *filename);
+int read_next_physical_record(zebraFile *z);
+int get_bytes(zebraFile *z, size_t size);
+int read_next_logical_record(zebraFile *z);
+int next_bank(zebraFile *z, bank *b);
+void zebra_close(zebraFile *z);
+
+#endif