From 1fb2d87c42ccef2231a595076db7cbf6c57dbd00 Mon Sep 17 00:00:00 2001
From: zorba <zorba@localhost>
Date: Thu, 18 Oct 2018 10:45:24 -0500
Subject: [PATCH] add .ch 181 support

---
 PyExpLabSys/file_parsers/chemstation.py | 48 +++++++++++++++++++++++--
 1 file changed, 46 insertions(+), 2 deletions(-)

diff --git a/PyExpLabSys/file_parsers/chemstation.py b/PyExpLabSys/file_parsers/chemstation.py
index a1ef060f..bbf77a1c 100644
--- a/PyExpLabSys/file_parsers/chemstation.py
+++ b/PyExpLabSys/file_parsers/chemstation.py
@@ -379,6 +379,7 @@ def __repr__(self):
 UINT16 = ENDIAN + 'H'
 INT16 = ENDIAN + 'h'
 INT32 = ENDIAN + 'i'
+UINT32 = ENDIAN + 'I'
 
 
 def parse_utf16_string(file_, encoding='UTF16'):
@@ -435,10 +436,13 @@ class CHFile(object):
         ('detector', 4213, 'utf16'),
         ('yscaling', 4732, ENDIAN + 'd')
     )
+    # Fields in version file version 181 are different for software info
+    fields_revtwo = tuple(filter(lambda x: x[1] not in [3601,3089,3802], fields))
+
     # The start position of the data
     data_start = 6144
     # The versions of the file format supported by this implementation
-    supported_versions = {179}
+    supported_versions = {179, 181}
 
     def __init__(self, filepath):
         """Instantiate object
@@ -450,7 +454,10 @@ def __init__(self, filepath):
         self.metadata = {}
         with open(self.filepath, 'rb') as file_:
             self._parse_header(file_)
-            self.values = self._parse_data(file_)
+            if self.metadata['magic_number_version'] == 179:
+                self.values = self._parse_data(file_)
+            elif self.metadata['magic_number_version'] == 181:
+                self.values = self._parse_data_decompress(file_)
 
     def _parse_header(self, file_):
         """Parse the header"""
@@ -461,6 +468,8 @@ def _parse_header(self, file_):
         if version not in self.supported_versions:
             raise ValueError('Unsupported file version {}'.format(version))
         self.metadata['magic_number_version'] = version
+        if version == 181:
+            self.fields = self.fields_revtwo
 
         # Parse all metadata fields
         for name, offset, type_ in self.fields:
@@ -548,6 +557,41 @@ def _parse_data(self, file_):
         file_.seek(self.data_start)
         return numpy.fromfile(file_, dtype='<d', count=n_points) * self.metadata['yscaling']
 
+    def _parse_data_decompress(self, file_):
+        """Parse the data"""
+        # from matlab implementation https://github.com/chemplexity/chromatography/blob/670ed772342a9c0440344682a02394a062c2467d/Methods/Import/ImportAgilent.m
+        # delta compressed data
+        # Go to the end of the file and calculate file length and number of datapoints
+        
+        file_.seek(0, 2)
+        n_points = (file_.tell() - self.data_start)        
+        file_length = file_.tell()
+        
+        buf = [0,0,0]
+        signal = [0] * int(n_points/2)
+        file_.seek(self.data_start)
+        count = 0        
+        
+        while file_.tell() < file_length:
+            buf[2] = unpack(INT16, file_.read(2))[0]
+            if buf[2] != 32767:
+                buf[1] = buf[1] + buf[2]
+                buf[0] = buf[0] + buf[1]
+            else:
+                buf[0] = unpack(INT16, file_.read(2))[0] * 4294967296.0
+                buf[0] = unpack(UINT32, file_.read(4))[0] + buf[0]
+                buf[1] = 0
+        
+            signal[count] = buf[0]
+            count += 1
+        
+        signal[count:] = []
+        
+        
+        # Return the data into a numpy array        
+        return numpy.array(signal) * self.metadata['yscaling']
+
+
     @cached_property
     def times(self):
         """The time values (x-value) for the data set in minutes"""