Release 0.9.0

.github/workflows/lint_and_test.yaml

@@ -15,7 +15,7 @@ jobs:
     # Name the job
     name: Lint and Test
     # Set the type of machine to run on
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-20.04
     steps:
         # Check out the latest commit from the current branch
       - name: Checkout Current Branch

CHANGELOG.md

@@ -6,6 +6,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.9.0] - 2024-03-26
+### Added
+- PNSSet class for parsing and writing `pnsSet.xml` files
+
+### Fixed
+- add ampSerialNumber and ampFirmwareVersion props to `FileInfo` class
+
 ## [0.8.0] - 2022-10-18
 ### Added
 - coordinates and sensor layout XML files for the Geodesic Head Web
@@ -90,7 +97,8 @@ In `Reader.get_physical_samples_from_epoch()`:
 - Parse key elements in categories.xml files with `mffpy.xml_files.Categories` class.
 - Incorporate `cached_property` dependency into `mffpy` library.
 
-[Unreleased]: https://github.com/bel-public/mffpy/compare/v0.8.0...HEAD
+[Unreleased]: https://github.com/bel-public/mffpy/compare/v0.9.0...HEAD
+[0.9.0]: https://github.com/bel-public/mffpy/compare/v0.8.0...v0.9.0
 [0.8.0]: https://github.com/bel-public/mffpy/compare/v0.7.4...v0.8.0
 [0.7.4]: https://github.com/bel-public/mffpy/compare/v0.7.3...v0.7.4
 [0.7.3]: https://github.com/bel-public/mffpy/compare/v0.7.2...v0.7.3

README.md

@@ -36,18 +36,18 @@ $ pre-commit install
 platform linux -- Python 3.6.7, pytest-7.0.1, pluggy-1.0.0
 rootdir: /home/runner/work/mffpy/mffpy
 plugins: cov-4.0.0
-collected 122 items
+collected 123 items
 
 mffpy/tests/test_cached_property.py ..                                   [  1%]
 mffpy/tests/test_devices.py .............                                [ 12%]
 mffpy/tests/test_dict2xml.py .                                           [ 13%]
 mffpy/tests/test_header_block.py ..                                      [ 14%]
-mffpy/tests/test_mffdir.py ....                                          [ 18%]
+mffpy/tests/test_mffdir.py ....                                          [ 17%]
 mffpy/tests/test_raw_bin_files.py ..................                     [ 32%]
 mffpy/tests/test_reader.py ......................                        [ 50%]
 mffpy/tests/test_writer.py ...........                                   [ 59%]
-mffpy/tests/test_xml_files.py .......................................... [ 94%]
-..                                                                       [ 95%]
+mffpy/tests/test_xml_files.py .......................................... [ 93%]
+...                                                                      [ 95%]
 mffpy/tests/test_zipfile.py .....                                        [100%]
 
 ----------- coverage: platform linux, python 3.6.7-final-0 -----------
@@ -68,23 +68,23 @@ mffpy/mffdir.py                                  92      7    92%
 mffpy/raw_bin_files.py                          113      0   100%
 mffpy/reader.py                                 110      2    98%
 mffpy/tests/__init__.py                           0      0   100%
-mffpy/tests/conftest.py                          11      0   100%
+mffpy/tests/conftest.py                          15      0   100%
 mffpy/tests/test_cached_property.py              33      0   100%
 mffpy/tests/test_devices.py                      12      0   100%
 mffpy/tests/test_dict2xml.py                     16      0   100%
 mffpy/tests/test_header_block.py                 33      0   100%
 mffpy/tests/test_mffdir.py                       30      0   100%
 mffpy/tests/test_raw_bin_files.py                63      0   100%
 mffpy/tests/test_reader.py                       96      0   100%
-mffpy/tests/test_writer.py                      204      0   100%
-mffpy/tests/test_xml_files.py                   202      1    99%
+mffpy/tests/test_writer.py                      212      0   100%
+mffpy/tests/test_xml_files.py                   214      1    99%
 mffpy/tests/test_zipfile.py                      34      0   100%
 mffpy/version.py                                  1      0   100%
 mffpy/writer.py                                  71      0   100%
-mffpy/xml_files.py                              554     18    97%
+mffpy/xml_files.py                              607     22    96%
 mffpy/zipfile.py                                 47      0   100%
 -----------------------------------------------------------------
-TOTAL                                          2023     40    98%
+TOTAL                                          2100     44    98%
 
 
 ============================= 122 passed in 7.19s ==============================

examples/example_2.json

@@ -3,6 +3,8 @@
         "mffVersion": "3",
         "acquisitionVersion": "5.4.1.2 (r28337)",
         "ampType": "NA400",
+        "ampFirmwareVersion": "1.6.23",
+        "ampSerialNumber": "M13010030",
         "recordTime": "2019-05-01T10:58:31.236065-07:00"
     },
     "dataInfo": {
@@ -8112,6 +8114,7 @@
         }
     },
     "dipoleSet": {},
+    "PNSSet": {},
     "historyEntries": [
         {
             "name": "Noise_30Seconds",

mffpy/tests/conftest.py

@@ -13,6 +13,7 @@
 ANY KIND, either express or implied.
 """
 
+from typing import Any, Dict
 from glob import glob
 import os.path as op
 from zipfile import ZipFile, ZIP_STORED
@@ -30,3 +31,49 @@ def ensure_mfz():
             for content_filename in glob(op.join(fname[:-3] + 'mff', '*')):
                 arc_filename = op.basename(content_filename)
                 zf.write(content_filename, arcname=arc_filename)
+
+
+@pytest.fixture
+def sensors() -> Dict[int, Any]:
+    return {
+        0: {
+            'name': 'ECG',
+            'number': 0,
+            'unit': 'uV',
+            'psgType': 0,
+            'mapping': 1,
+            'samplingRate': 0,
+            'sensorType': 'ECG',
+            'highpass': 0.3000000119,
+            'lowpass': 70,
+            'notch': 60,
+            'groupNumber': 1,
+            'gain': 1,
+            'defaultDisplayAmplitude': 7.5,
+            'highpassDisplay': 0.3000000119,
+            'lowpassDisplay': 70,
+            'notchDisplay': 60,
+            'color':  [0.0000, 0.0000, 0.0000, 1.0000],
+            'positiveUp': 'false',
+        },
+        1: {
+            'name': 'EMG',
+            'number': 1,
+            'unit': 'uV',
+            'psgType': 0,
+            'mapping': 2,
+            'samplingRate': 0,
+            'sensorType': 'EMG',
+            'highpass': 10,
+            'lowpass': 100,
+            'notch': 60,
+            'groupNumber': 1,
+            'gain': 1,
+            'defaultDisplayAmplitude': 7.5,
+            'highpassDisplay': 10,
+            'lowpassDisplay': 100,
+            'notchDisplay': 60,
+            'color': [0.0000, 0.0000, 0.0000, 1.0000],
+            'positiveUp': 'false',
+        }
+    }

mffpy/tests/test_writer.py

@@ -165,7 +165,7 @@ def test_overwrite_mfz(tmpdir):
         assert R2.startdatetime == time2
 
 
-def test_writer_writes_multple_bins(tmpdir):
+def test_writer_writes_multple_bins(tmpdir, sensors):
     """test that `mffpy.Writer` can write multiple binary files"""
     dirname = join(str(tmpdir), 'multiple_bins.mff')
     device = 'HydroCel GSN 256 1.0'
@@ -174,7 +174,7 @@ def test_writer_writes_multple_bins(tmpdir):
     sampling_rate = 128
     num_channels_dict = {
         'EEG': 256,
-        'PNSData': 16
+        'PNSData': 2
     }
     data = {
         dtype: np.random.randn(
@@ -192,6 +192,12 @@ def test_writer_writes_multple_bins(tmpdir):
     startdatetime = datetime.strptime(
         '1984-02-18T14:00:10.000000+0100', XML._time_format)
     W.addxml('fileInfo', recordTime=startdatetime)
+    W.addxml(
+        'PNSSet',
+        name='Physio 16 set 60hz 1.0',
+        amp_series='400',
+        sensors=sensors,
+    )
     W.add_coordinates_and_sensor_layout(device)
     for b in bin_writers.values():
         W.addbin(b)
@@ -212,6 +218,14 @@ def test_writer_writes_multple_bins(tmpdir):
     layout = XML.from_file(layout)
     assert layout.name == device
 
+    pns_set = R.directory.filepointer('pnsSet')
+    pns_set = XML.from_file(pns_set)
+    assert pns_set.name == 'Physio 16 set 60hz 1.0'
+    assert pns_set.amp_series == '400'
+    for key, val in pns_set.sensors.items():
+        for k, v in val.items():
+            assert v == sensors[key][k]
+
 
 def test_write_multiple_blocks():
     """check that BinWriter correctly handles adding multiple blocks"""

mffpy/tests/test_xml_files.py

@@ -30,6 +30,7 @@
 
 examples_path = join(dirname(__file__), '..', '..', 'examples')
 mff_path = join(examples_path, 'example_1.mff')
+mffpath_3 = join(examples_path, 'example_3.mff')
 
 """
 Here are several fixtures that parse example xml files
@@ -146,6 +147,8 @@ def test_FileInfo(file_info):
     assert file_info.mffVersion == '3'
     assert file_info.acquisitionVersion == '5.4.1.2 (r28337)'
     assert file_info.ampType == 'NA400'
+    assert file_info.ampSerialNumber == 'M13010030'
+    assert file_info.ampFirmwareVersion == '1.6.23'
     expected_rt = datetime.strptime(
         '2019-05-01T10:58:31.236065-0700', "%Y-%m-%dT%H:%M:%S.%f%z")
     assert file_info.recordTime == expected_rt, f"""
@@ -516,6 +519,18 @@ def test_dipoleSet_w_different_order(dipoleSet):
     ], dtype=np.float32))
 
 
+def test_pnsSet(sensors):
+    """test parsing of `pnsSet.xml`"""
+    filepath = join(mffpath_3, 'pnsSet.xml')
+    assert exists(filepath), f"Not found: '{filepath}'"
+    pns_set = XML.from_file(filepath)
+    assert pns_set.name == 'Physio 16 set 60hz 1.0'
+    assert pns_set.amp_series == '400'
+    for key, val in pns_set.sensors.items():
+        for k, v in val.items():
+            assert v == sensors[key][k]
+
+
 @pytest.mark.parametrize("idx,expected", [
     ('name', 'Noise_30Seconds'),
     ('method', 'Segmentation'),

mffpy/version.py

@@ -1 +1 @@
-__version__ = "0.8.0"
+__version__ = "0.9.0"