Merge pull request #2 from gitrust/docker

Additional fields and fixes

Author: gitrust

.gitignore

@@ -1 +1,3 @@
-*~
+*~
+__pycache__
+.pytest_cache

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "python.formatting.provider": "black"
+}

Makefile

@@ -0,0 +1,3 @@
+
+info:
+	python scpinfo.py example/example.scp

scp.py

@@ -137,8 +137,12 @@ class Section2(Section):
     def __init__(self, header, pointer):
         super().__init__(header)
         self.p = pointer
+        # Number of Huffman Tables defined (if 19 999 then the default table, defined in C.3.7.6, is used).
+        self.nr_huffman_tables = 0
+        # Number of code structures in table # 1
+        self.nr_code_struct = 0
 
-
+        
 class Section3(Section):
     """Section 3 - ECG Leads definition"""
     def __init__(self, header, pointer):
@@ -152,14 +156,19 @@ def __init__(self, header, pointer):
         self.nr_leads_sim = 0
         self.leads = []
 
-
+# QRS Locations if reference beats are encoded
 class Section4(Section):
-    """Section 4 - Reserved for legacy SCP-ECG versions"""
+    """Section 4 - Reserved for legacy SCP-ECG versions (SCP Versions 1.x, 2.x)"""
     def __init__(self, header, pointer):
         super().__init__(header)
         self.p = pointer
-
-
+        # Length of reference beat type 0 in milliseconds
+        self.ref_beat_type_len = 0
+        # Sample number of the fiducial point (QRS trigger point), with respect to beginning of reference beat type 0
+        self.sample_nr_fidpoint = 0
+        # Total number of QRS complexes within the entire short-term ECG rhythm record
+        self.total_nr_qrs = 0
+        
 class Section5(Section):
     """Section 5 with samples"""
     def __init__(self, header, pointer):
@@ -206,6 +215,19 @@ def __init__(self, header, pointer):
         super().__init__(header)
         self.p = pointer
 
+        self.reference_count = 0
+        # number of pacemaker spikes
+        self.pace_count = 0
+        # Average RR interval in milliseconds for all QRS's
+        self.rr_interval = 0
+        # Average PP interval in milliseconds for all QRS's
+        self.pp_interval = 0
+        self.pace_times = []
+        self.pace_amplitudes = []
+        self.pace_types = []
+        self.pace_sources = []
+        self.pace_indexes = []
+        self.pace_widths = []
 
 class Section8(Section):
     """Section 8 - Textual diagnosis"""

scpformat.py

@@ -5,7 +5,7 @@
     SCP section and attribute formatter
 """
 
-from scputil import b2i, bdecode, lead_dic
+from scputil import b2i, b2s, bdecode, lead_dic
 
 
 class Section1TagsFormatter:
@@ -129,7 +129,7 @@ def __init__(self, bytes):
         self._print = False
         if bytes:
             # in minutes
-            self.offset = b2i(bytes[0:2])
+            self.offset = b2s(bytes[0:2])
             self.index = b2i(bytes[2:4])
             self.desc = bdecode(bytes[4:])
             self._print = True
@@ -402,6 +402,7 @@ def format_section2(s2, printer):
     print()
     printer.p('--Section2--', '----')
     format_header(s2.h, printer)
+    printer.p('NrHuffmanTables', '19999 (default table)' if s2.nr_huffman_tables == 19999 else s2.nr_huffman_tables)
 
 
 def format_section3(s3, printer):
@@ -416,7 +417,6 @@ def format_section3(s3, printer):
     printer.p('LeadCount', len(s3.leads))
     LeadIdFormatter(s3.leads).format(printer)
 
-
 def format_section5(s5, printer):
     if not s5.p.section_has_data():
         return
@@ -495,15 +495,22 @@ def format_section7(s7, printer):
     print()
     printer.p('--Section7--', '----')
     format_header(s7.h, printer)
+    printer.p('ReferenceCount', s7.reference_count)
+    printer.p('PaceCount', s7.pace_count)
+    printer.p('Avg RR Interval (ms)', "29999 (not calculated)" if 29999 == s7.rr_interval else s7.rr_interval )
+    printer.p('Avg PP Interval (ms)', "29999 (not calculated)" if 29999 == s7.pp_interval else s7.pp_interval)
 
 
-def format_section4(s4, printer):
-    if not s4.p.section_has_data():
+def format_section4(s, printer):
+    if not s.p.section_has_data():
         return
-
+    
     print()
     printer.p('--Section4--', '----')
-    format_header(s4.h, printer)
+    format_header(s.h, printer)
+    printer.p('RefBeatType0Len', s.ref_beat_type_len)
+    printer.p('SampleNr FiducialPoint', s.sample_nr_fidpoint)
+    printer.p('TotalNrQRS', s.total_nr_qrs)
 
 
 def format_section8(s8, printer):

scpreader.py

@@ -40,6 +40,34 @@ def readint(self, n):
             return int(value)
         return int.from_bytes(bytes, 'little')
 
+    def read_byte(self):
+        """Read 1 byte (little endian)"""
+        bytes = self.file.read(1)
+        if len(bytes) == 0:
+            print('ERR: Could not read_byte, corrupt structure. File position ' + self.pos())
+        return struct.unpack("<B", bytes)[0]
+
+    def read_ushort(self):
+        """Read 2 bytes as unsigned short (little endian)"""
+        bytes = self.file.read(2)
+        if len(bytes) == 0:
+            print('ERR: Could not read_ushort, corrupt structure. File position ' + self.pos())
+        return struct.unpack("<H", bytes)[0]
+
+    def read_uint(self):
+        """Read 4 bytes as unsigned integer (little endian)"""
+        bytes = self.file.read(4)
+        if len(bytes) == 0:
+            print('ERR: Could not read_uint, corrupt structure. File position ' + self.pos())
+        return struct.unpack("<I", bytes)[0]
+
+    def read_ulong(self):
+        """Read 6 bytes as unsigned long (little endian)"""
+        bytes = self.file.read(6)
+        if len(bytes) == 0:
+            print('ERR: Could not read_ulong, corrupt structure. File position ' + self.pos())
+        return struct.unpack("<Q", bytes)[0]
+
     def move(self, n):
         """move n bytes from beginning of file"""
         return self.file.seek(n, 0)
@@ -68,8 +96,8 @@ def close(self):
     def read_scp(self):
         """Read an scp file into memory and returns a ScpRecord"""
         scpRecord = ScpRecord()
-        scpRecord.crc = self.reader.readint(2)
-        scpRecord.len = self.reader.readint(4)
+        scpRecord.crc = self.reader.read_ushort()
+        scpRecord.len = self.reader.read_uint()
 
         s0 = self._section0()
         scpRecord.sections.append(s0)
@@ -93,9 +121,9 @@ def read_scp(self):
     def _sectionheader(self):
         """Read and return a section header"""
         header = SectionHeader()
-        header.crc = self.reader.readint(2)
-        header.id = self.reader.readint(2)
-        header.len = self.reader.readint(4)
+        header.crc = self.reader.read_ushort()
+        header.id = self.reader.read_ushort()
+        header.len = self.reader.read_uint()
         header.versnr = self.reader.readint(1)
         header.protnr = self.reader.readint(1)
         header.reserved = self.reader.reads(6)
@@ -107,11 +135,11 @@ def _sectionheader(self):
     def _sectionpointer(self):
         """Read and return a section pointer"""
         p = SectionPointer()
-        p.id = self.reader.readint(2)
+        p.id = self.reader.read_ushort()
         # section length
-        p.len = self.reader.readint(4)
+        p.len = self.reader.read_uint()
         # index of section starting from zero
-        p.index = self.reader.readint(4)
+        p.index = self.reader.read_uint()
         return p
 
     def _section0(self):
@@ -139,8 +167,8 @@ def _section0(self):
     def _readtag(self):
         """Read and return a scp tag"""
         tag = Tag()
-        tag.tag = self.reader.readint(1)
-        tag.len = self.reader.readint(2)
+        tag.tag = self.reader.read_byte()
+        tag.len = self.reader.read_ushort()
 
         if tag.len > 0:
             tag.data = self.reader.read(tag.len)
@@ -149,9 +177,9 @@ def _readtag(self):
     def _readleadid(self):
         """Read and return a LeadId"""
         leadid = LeadIdentification()
-        leadid.startsample = self.reader.readint(4)
-        leadid.endsample = self.reader.readint(4)
-        leadid.leadid = self.reader.readint(1)
+        leadid.startsample = self.reader.read_uint()
+        leadid.endsample = self.reader.read_uint()
+        leadid.leadid = self.reader.read_byte()
         return leadid
 
     def _read_section(self, pointer, nr_of_leads):
@@ -206,6 +234,10 @@ def _section2(self, pointer):
 
         header = self._sectionheader()
         s = Section2(header, pointer)
+
+        s.nr_huffman_tables = self.reader.read_ushort()
+        # Number of code structures in table # 1
+        s.nr_code_struct = self.reader.read_ushort()
         return s
 
     def _section3(self, pointer):
@@ -215,8 +247,8 @@ def _section3(self, pointer):
         header = self._sectionheader()
         s = Section3(header, pointer)
 
-        s.nrleads = self.reader.readint(1)
-        s.flags = self.reader.readint(1)
+        s.nrleads = self.reader.read_byte()
+        s.flags = self.reader.read_byte()
         # first bit
         s.ref_beat_substr = bool(s.flags >> 1 & 1)
         # bits 3-7
@@ -235,6 +267,10 @@ def _section4(self, pointer):
         header = self._sectionheader()
         s = Section4(header, pointer)
 
+        s.ref_beat_type_len = self.reader.read_ushort()
+        s.sample_nr_fidpoint = self.reader.read_ushort()
+        s.total_nr_qrs = self.reader.read_ushort()
+
         return s
 
     def _section5(self, pointer, nr_of_leads):
@@ -244,14 +280,14 @@ def _section5(self, pointer, nr_of_leads):
         header = self._sectionheader()
         s = Section5(header, pointer)
 
-        s.avm = self.reader.readint(2)
-        s.sample_time_interval = self.reader.readint(2)
-        s.sample_encoding = self.reader.readint(1)
-        s.reserved = self.reader.readint(1)
+        s.avm = self.reader.read_ushort()
+        s.sample_time_interval = self.reader.read_ushort()
+        s.sample_encoding = self.reader.read_byte()
+        s.reserved = self.reader.read_byte()
 
         # nr of bytes for each lead
         for _ in range(0, nr_of_leads):
-            s.nr_bytes_for_leads.append(self.reader.readint(2))
+            s.nr_bytes_for_leads.append(self.reader.read_ushort())
 
         # samples for each lead
         for nr in s.nr_bytes_for_leads:
@@ -261,7 +297,7 @@ def _section5(self, pointer, nr_of_leads):
             samples_len = nr / 2
 
             while samples_len > 0:
-                data.samples.append(self.reader.readint(2))
+                data.samples.append(self.reader.read_ushort())
                 samples_len = samples_len - 1
 
             s.data.append(data)
@@ -275,16 +311,18 @@ def _section6(self, pointer, nr_of_leads):
         header = self._sectionheader()
         s = Section6(header, pointer)
 
-        s.avm = self.reader.readint(2)
-        s.sample_time_interval = self.reader.readint(2)
-        s.sample_encoding = self.reader.readint(1)
-        s.bimodal_compression = self.reader.readint(1)
+        s.avm = self.reader.read_ushort()
+        s.sample_time_interval = self.reader.read_ushort()
+        s.sample_encoding = self.reader.read_byte()
+        s.bimodal_compression = self.reader.read_byte()
 
 
         # nr of bytes for each lead
         for _ in range(0, nr_of_leads):
-            s.nr_bytes_for_leads.append(self.reader.readint(2))
+            s.nr_bytes_for_leads.append(self.reader.read_ushort())
 
+        # TODO: check if section2 exists -> samples are Huffman encoded
+        
         # samples for each lead
         for nr in s.nr_bytes_for_leads:
             data = DataSamples()
@@ -293,6 +331,7 @@ def _section6(self, pointer, nr_of_leads):
             samples_len = nr / 2
 
             while samples_len > 0:
+                # signed 2byte integers
                 data.samples.append(self.reader.readint(2))
                 samples_len = samples_len - 1
 
@@ -306,6 +345,20 @@ def _section7(self, pointer):
         header = self._sectionheader()
         s = Section7(header, pointer)
 
+        s.reference_count = self.reader.read_byte()
+        s.pace_count = self.reader.read_byte()
+        s.rr_interval = self.reader.read_ushort()
+        s.pp_interval = self.reader.read_ushort()
+        for i in range(0, s.pace_count):
+            s.pace_times[i] = self.reader.readint(2)
+            s.pace_amplitudes[i] = self.reader.read_ushort()
+        
+        for i in range(0, s.pace_count):
+            s.pace_types = self.reader.read_byte()
+            s.pace_sources = self.reader.read_byte()
+            s.pace_indexes = self.reader.readint(2)
+            s.pace_widths = self.reader.readint(2)
+
         return s
 
 

scputil.py

@@ -1,12 +1,25 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
+import struct
 
+def b2s(bytes):
+    if len(bytes) != 2:
+        raise ValueError("bytes must be exactly 2 bytes long")
+    return struct.unpack('h', bytes)
+
+def b2b(bytes):
+    if len(bytes) != 1:
+        raise ValueError("bytes must be exactly 1 byte long")
+    return struct.unpack('B', bytes)
 
 def b2i(bytes):
-    """Convert bytes to int (little endian)"""
+    """Convert bytes to unsigned integer (little endian)"""
     return int.from_bytes(bytes, 'little')
 
+def b2si(bytes):
+    """Convert bytes to signed integer (little endian)"""
+    return int.from_bytes(bytes, 'little', signed=True)
 
 def bdecode(bytes):
     """Decode bytes as iso-8859-1 and remove null terminators"""