From 0ecf802ac4cd01f9fad04da19179bb1334d5a6f2 Mon Sep 17 00:00:00 2001
From: Matthew Einhorn <moiein2000@gmail.com>
Date: Mon, 23 Dec 2019 15:18:05 -0500
Subject: [PATCH] Use handshake length for alignment.

---
 ceed/analysis/merge_data.py | 18 ++++++++++++++----
 ceed/storage/controller.py  | 30 ++++++++++++++++++++----------
 2 files changed, 34 insertions(+), 14 deletions(-)

diff --git a/ceed/analysis/merge_data.py b/ceed/analysis/merge_data.py
index 6b8faf7..f649d31 100644
--- a/ceed/analysis/merge_data.py
+++ b/ceed/analysis/merge_data.py
@@ -18,6 +18,7 @@
 import numpy as np
 import nixio as nix
 from base_kivy_app.utils import yaml_dumps, yaml_loads
+from ceed.storage.controller import num_ticks_handshake
 
 __all__ = ('CeedMCSDataMerger', 'DigitalDataStore', 'MCSDigitalData',
            'CeedDigitalData', 'AlignmentException')
@@ -31,6 +32,8 @@ class AlignmentException(Exception):
 
 class DigitalDataStore(object):
 
+    counter_bit_width = 32
+
     short_count_indices = None
 
     short_count_data = None
@@ -54,12 +57,14 @@ class DigitalDataStore(object):
     came from.
     '''
 
-    def __init__(self, short_count_indices, count_indices, clock_index):
+    def __init__(self, short_count_indices, count_indices, clock_index,
+                 counter_bit_width):
         '''indices are first mapped with projector_to_aquisition_map. '''
         super(DigitalDataStore, self).__init__()
         self.short_count_indices = short_count_indices
         self.count_indices = count_indices
         self.clock_index = clock_index
+        self.counter_bit_width = counter_bit_width
         self.populate_indices()
 
     def populate_indices(self):
@@ -332,12 +337,14 @@ def create_or_reuse_ceed_data_container(self):
         short_count_indices = config['short_count_indices']
         count_indices = config['count_indices']
         clock_index = config['clock_idx']
+        counter_bit_width = config['counter_bit_width']
 
         if self.ceed_data_container is None or not self.ceed_data_container.\
             compare_indices(
                 short_count_indices, count_indices, clock_index):
             self.ceed_data_container = CeedDigitalData(
-                short_count_indices, count_indices, clock_index)
+                short_count_indices, count_indices, clock_index,
+                counter_bit_width)
         return self.ceed_data_container
 
     def create_or_reuse_mcs_data_container(self):
@@ -348,12 +355,14 @@ def create_or_reuse_mcs_data_container(self):
         short_count_indices = map_f(config['short_count_indices'])
         count_indices = map_f(config['count_indices'])
         clock_index = map_f(config['clock_idx'])
+        counter_bit_width = config['counter_bit_width']
 
         if self.mcs_data_container is None or not self.mcs_data_container.\
             compare_indices(
                 short_count_indices, count_indices, clock_index):
             self.mcs_data_container = MCSDigitalData(
-                short_count_indices, count_indices, clock_index)
+                short_count_indices, count_indices, clock_index,
+                counter_bit_width)
         return self.mcs_data_container
 
     def parse_ceed_digital_data(self):
@@ -372,9 +381,10 @@ def get_alignment(self, find_by=None, force=False):
         mcs = self.mcs_data_container
 
         s = 0
-        # counter_bit_width = 32
+        counter_bit_width = ceed_.counter_bit_width
         if find_by is None:  # find by uuid
             # n is number of frames we need to send uuid
+            n = num_ticks_handshake(counter_bit_width, ceed_.count_indices, 16)
             n = int(ceil(32 / float(len(ceed_.count_indices)))) * 5
 
             # following searches for the uuid in the mcs data
diff --git a/ceed/storage/controller.py b/ceed/storage/controller.py
index 6c99913..9b084db 100644
--- a/ceed/storage/controller.py
+++ b/ceed/storage/controller.py
@@ -34,7 +34,7 @@
 from base_kivy_app.app import app_error
 from base_kivy_app.utils import yaml_dumps, yaml_loads
 
-__all__ = ('CeedDataWriterBase', 'DataSerializerBase')
+__all__ = ('CeedDataWriterBase', 'DataSerializerBase', 'num_ticks_handshake')
 
 
 class CeedDataWriterBase(EventDispatcher):
@@ -939,12 +939,22 @@ def num_ticks_handshake(self, config_len):
 
         :param config_len: The number of config **bytes** being sent.
         """
-        num_bytes = self.counter_bit_width // 8
-        # the message + padding in bytes
-        config_len += num_bytes - (config_len % num_bytes)
-        config_len //= num_bytes  # in
-        config_len += 1  # the message length byte
-
-        ticks_per_int = int(
-            ceil(self.counter_bit_width / len(self.count_indices)))
-        return config_len * ticks_per_int * 2 + 2
+        return num_ticks_handshake(
+            self.counter_bit_width, self.count_indices, config_len)
+
+
+def num_ticks_handshake(counter_bit_width, count_indices, config_len):
+    """Gets the number of ticks required to transmit the handshake
+    signature of the experiment as provided to :meth:`get_bits` with
+    ``config_bytes``.
+
+    :param config_len: The number of config **bytes** being sent.
+    """
+    num_bytes = counter_bit_width // 8
+    # the message + padding in bytes
+    config_len += num_bytes - (config_len % num_bytes)
+    config_len //= num_bytes  # in
+    config_len += 1  # the message length byte
+
+    ticks_per_int = int(ceil(counter_bit_width / len(count_indices)))
+    return config_len * ticks_per_int * 2 + 2