From b619d35ce4dd4262701adebb2f2c8dbb91aeec55 Mon Sep 17 00:00:00 2001
From: Jim Rybarski <jim@rybarski.com>
Date: Sat, 30 Aug 2014 09:33:49 -0500
Subject: [PATCH] gets chunk labels and pointers

---
 nd2reader/__init__.py | 75 +++++++++++++++++++++++++++++++++++++++----
 1 file changed, 68 insertions(+), 7 deletions(-)

diff --git a/nd2reader/__init__.py b/nd2reader/__init__.py
index bf83a19..2df8a28 100644
--- a/nd2reader/__init__.py
+++ b/nd2reader/__init__.py
@@ -1,7 +1,8 @@
 import array
 import numpy as np
+import re
 import struct
-import StringIO
+from pprint import pprint
 
 
 class Nd2Reader(object):
@@ -12,25 +13,85 @@ class Nd2Reader(object):
     def __init__(self, filename):
         self._filename = filename
         self._file_handler = None
+        self._chunk_map_start_location = None
+        self._map_keys = {}
+        self._read_map()
 
     @property
-    def file_handler(self):
+    def fh(self):
         if self._file_handler is None:
             self._file_handler = open(self._filename, "rb")
         return self._file_handler
 
+    def _read_map(self):
+        """
+        Every label ends with an exclamation point, however, we can't directly search for those to find all the labels
+        as some of the bytes contain the value 33, which is the ASCII code for "!". So we iteratively find each label,
+        grab the subsequent data (always 16 bytes long), advance to the next label and repeat.
+
+        """
+        raw_text = self.raw_chunk_map_text
+        label_start = self._find_first_label_offset(raw_text)
+        while True:
+            data_start = self._get_data_start(label_start, raw_text)
+            label, value = self._extract_map_key(label_start, data_start, raw_text)
+            if label == "ND2 CHUNK MAP SIGNATURE 0000001!":
+                # We've reached the end of the chunk map
+                break
+            self._map_keys[label] = value
+            label_start = data_start + 16
+
+    @staticmethod
+    def _find_first_label_offset(raw_text):
+        """
+        The chunk map starts with some number of (seemingly) useless bytes, followed
+        by "ND2 FILEMAP SIGNATURE NAME 0001!". We return the location of the first character after this sequence,
+        which is the actual beginning of the chunk map.
+
+        """
+        return raw_text.index("ND2 FILEMAP SIGNATURE NAME 0001!") + 32
+
+    @staticmethod
+    def _get_data_start(label_start, raw_text):
+        """
+        The data for a given label begins immediately after the first exclamation point
+
+        """
+        return raw_text.index("!", label_start) + 1
+
+    @staticmethod
+    def _extract_map_key(label_start, data_start, raw_text):
+        """
+        Chunk map entries are a string label of arbitrary length followed by 16 bytes of data, which represent
+        the byte offset from the beginning of the file where that data can be found.
+
+        """
+        key = raw_text[label_start: data_start]
+        value = struct.unpack("QQ", raw_text[data_start: data_start + 16])
+        return key, value
+
     @property
-    def chunk_map_location(self):
+    def chunk_map_start_location(self):
         """
         The position in bytes from the beginning of the file where the chunk map begins.
         The chunk map is a series of string labels followed by the position (in bytes) of the respective data.
 
         """
-        self.file_handler.seek(-8, 2)
-        return struct.unpack("Q", self.file_handler.read(8))[0]
+        if self._chunk_map_start_location is None:
+            # Put the cursor 8 bytes before the end of the file
+            self.fh.seek(-8, 2)
+            # Read the last 8 bytes of the file
+            self._chunk_map_start_location = struct.unpack("Q", self.fh.read(8))[0]
+        return self._chunk_map_start_location
 
-    def read_chunk(self, location):
-        pass
+    @property
+    def raw_chunk_map_text(self):
+        """
+        Reads the entire chunk map and returns it as a string.
+
+        """
+        self.fh.seek(self.chunk_map_start_location)
+        return self.fh.read(-1)
 
     @staticmethod
     def as_numpy_array(arr):