Fix/pressure parser error (#17)

* added an integration tests revealing parser bug

* Revert "Merge pull request #11 from MideTechnology/feature/10_parser-optimization"

This reverts commit a045a8e, reversing
changes made to aefe43d.

* Revert "Revert "Merge pull request #11 from MideTechnology/feature/10_parser-optimization""

This reverts commit aeff0ad.

The original reversion confirms that the issue is not related to
archive/#11; with that confirmed, the original reversion may be removed

* removed code causing deprecation warnings

* manually specified in numpy parser standardized mapping from struct to numpy typestrings

* added sanity checks for integrity of typestring conversions

* moved typestring assertion to unit tests

idelib/importer.py

@@ -603,7 +603,7 @@ def getExitCondition(recording, bytesRead=1000):
         if idx <= len(data):
             result = data[idx]
     except (IOError, IndexError, ValueError) as e:
-        logger.warn(e)
+        logger.warning(e)
 
     recording.seek(offset)
     return result        

idelib/parsers.py

@@ -889,7 +889,6 @@ def getHeader(self):
 
 
 class ChannelDataArrayBlock(ChannelDataBlock):
-
     def __init__(self, element):
         super(ChannelDataArrayBlock, self).__init__(element)
         self._payload = None
@@ -905,6 +904,34 @@ def payload(self):
             self._payloadEl.gc()
         return self._payload
 
+    # Define standard mapping from struct to numpy typestring
+    #   (conversions taken from struct & numpy docs:)
+    #   https://docs.python.org/3/library/struct.html#format-characters
+    #   https://numpy.org/doc/stable/reference/arrays.dtypes.html#specifying-and-constructing-data-types
+    TO_NP_TYPESTR = {
+        # 'x': '',
+        'c': 'b',
+        'b': 'b',
+        'B': 'B',
+        '?': '?',
+        'h': 'i2',
+        'H': 'u2',
+        'i': 'i4',
+        'I': 'u4',
+        'l': 'i4',
+        'L': 'u4',
+        'q': 'i8',
+        'Q': 'u8',
+        # 'n': '',
+        # 'N': '',
+        # 'e': 'f2',  unsupported in Python3.5
+        'f': 'f4',
+        'd': 'f8',
+        # 's': '',
+        # 'p': '',
+        # 'P': '',
+    }
+
     def parseWith(self, parser, start=None, end=None, step=1, subchannel=None):
         """ Parse an element's payload. Use this instead of directly using
             `parser.parse()` for consistency's sake.
@@ -941,13 +968,13 @@ def parseWith(self, parser, start=None, end=None, step=1, subchannel=None):
             else:
                 endian = '>'
 
-            streamDtype = np.dtype(
-                ','.join([endian+typeId for typeId in parser_format])
-            )
+            streamDtype = np.dtype(','.join([
+                endian + self.TO_NP_TYPESTR[typeId] for typeId in parser_format
+            ]))
 
             isHomogeneous = len(set(parser_format)) == 1
             if isHomogeneous:
-                commonDtype = np.dtype(endian + parser_format[0])
+                commonDtype = np.dtype(endian + self.TO_NP_TYPESTR[parser_format[0]])
             else:
                 commonDtype = None
 

testing/test_integration.py

@@ -0,0 +1,42 @@
+import os.path
+
+import pytest  # type: ignore
+import idelib
+
+
+@pytest.mark.parametrize('filename', [
+    os.path.join('testing', 'test3.IDE'),
+])
+def test_integ_channels(filename):
+    with idelib.importFile(filename) as ds:
+        assert {i for i in ds.channels.keys()} == {8, 36, 59, 70, 80, 84}
+
+        accel100g_ch = ds.channels[8]
+        data = accel100g_ch.getSession().arraySlice()
+        assert data.shape[0] == 5  # t, x, y, z, mic
+        assert data.size > 0
+
+        accel40g_ch = ds.channels[80]
+        data = accel40g_ch.getSession().arraySlice()
+        assert data.shape[0] == 4  # t, x, y, z
+        assert data.size > 0
+
+        rot_ch = ds.channels[84]
+        data = rot_ch.getSession().arraySlice()
+        assert data.shape[0] == 4  # t, x, y, z
+        assert data.size > 0
+
+        orient_ch = ds.channels[70]
+        data = orient_ch.getSession().arraySlice()
+        assert data.shape[0] == 5  # t, x, y, z, w
+        assert data.size > 0
+
+        pt_ch = ds.channels[36]
+        data = pt_ch.getSession().arraySlice()
+        assert data.shape[0] == 3  # t, press, temp
+        assert data.size > 0
+
+        pt_ctrl_ch = ds.channels[59]
+        data = pt_ctrl_ch.getSession().arraySlice()
+        assert data.shape[0] == 3  # t, press, temp
+        assert data.size > 0

testing/test_parsers.py

@@ -1,5 +1,6 @@
 import unittest
 import mock
+import struct
 
 from ebmlite.core import *  # type: ignore
 import numpy as np  # type: ignore
@@ -107,6 +108,14 @@ def testParseMinMeanMax(self):
     def testGetHeader(self):
         self.assertEqual(self.block.getHeader(), (211, 32))
 
+    def testToNpTypestr(self):
+        for stype, nptype in ChannelDataArrayBlock.TO_NP_TYPESTR.items():
+            for endian in ('<', '>'):
+                assert (
+                    struct.calcsize(endian+stype)
+                    == np.dtype(endian+nptype).itemsize
+                )
+
     def testParseWith(self):
         parser = self.doc.channels[32].parser