MRG+1: GDF support (#4205)

* WIP: add basic GDF1 and GDF2 support

only tested on a few GDF test files
doesn't break existing EDF tests

* Remove \x00 from channel names

* Fix data calibration

- Unified offset and calibration values for EDF/BDF/GDF modules
- few PEP8 fixes
- TODO: GDF 2.x triggers are detected as multiples of 256
- TODO: overflow and saturation detection

* Proper imports imports in test_gdf.py

* Fix to test_edf.py

An additional warning has been added in edf.py when Lowpass information
is not available in file header.

As a result test_stim_channel() would fail. The test should now expect
2 warnings.

* Separated EDF and GDF code

- EDF and GDF file headers are now read in their own private subfunction
- some PEP8 and cosmetic changes
- GDF events are still multiples of 256

* Add biosig GDF test file

make Travis happy

* python3 fixes

- python3 requires decoding the bytes objects to produce strings
- np.unique() fails for dtype=object in python3 (see
numpy/numpy#641)
- flake, pydocstyle

* Read biosemi GDF stim_channel properly

* Speed up reading from file

- fromstring -> fromfile

* Test routines and added safechecks

Also remove test datafiles (see
mne-tools/mne-testing-data#23)

* Update utils, and missing lowpass info no longer issues warning

* Added stim_channel argument check

* Address comments

* Address comments and update doc

* Address comments

* Docstyle

doc/manual/io.rst

@@ -23,6 +23,7 @@ EEG                   Brainvision                .vhdr      :func:`mne.io.read_r
 EEG                   Neuroscan CNT              .cnt       :func:`mne.io.read_raw_cnt`
 EEG                   European data format       .edf       :func:`mne.io.read_raw_edf`
 EEG                   Biosemi data format        .bdf       :func:`mne.io.read_raw_edf`
+EEG                   General data format        .gdf       :func:`mne.io.read_raw_edf`
 EEG                   EGI simple binary          .egi       :func:`mne.io.read_raw_egi`
 EEG                   EEGLAB                     .set       :func:`mne.io.read_raw_eeglab` and :func:`mne.read_epochs_eeglab`
 Electrode locations   elc, txt, csd, sfp, htps   Misc       :func:`mne.channels.read_montage`
@@ -262,26 +263,37 @@ European data format (.edf)
 
 EDF and EDF+ files can be read in using :func:`mne.io.read_raw_edf`.
 
-http://www.edfplus.info/specs/edf.html
+`EDF (European Data Format) <http://www.edfplus.info/specs/edf.html>`_ and
+`EDF+ <http://www.edfplus.info/specs/edfplus.html>`_ are 16-bit formats.
 
-EDF (European Data Format) and EDF+ are 16-bit formats
-http://www.edfplus.info/specs/edfplus.html
-
-The EDF+ files may contain an annotation channel which can
-be used to store trigger information. The Time-stamped Annotation
-Lists (TALs) on the annotation  data can be converted to a trigger
-channel (STI 014) using an annotation map file which associates
-an annotation label with a number on the trigger channel.
+The EDF+ files may contain an annotation channel which can be used to store
+trigger information. The Time-stamped Annotation Lists (TALs) on the
+annotation  data can be converted to a trigger channel (STI 014) using an
+annotation map file which associates an annotation label with a number on
+the trigger channel.
 
 Biosemi data format (.bdf)
 ==========================
 
-The BDF format (http://www.biosemi.com/faq/file_format.htm) is a 24-bit variant
-of the EDF format used by the EEG systems manufactured by a company called
-BioSemi. It can also be read in using :func:`mne.io.read_raw_edf`.
+The `BDF format <http://www.biosemi.com/faq/file_format.htm>`_ is a 24-bit
+variant of the EDF format used by the EEG systems manufactured by a company
+called BioSemi. It can also be read in using :func:`mne.io.read_raw_edf`.
 
 .. warning:: The data samples in a BDF file are represented in a 3-byte (24-bit) format. Since 3-byte raw data buffers are not presently supported in the fif format these data will be changed to 4-byte integers in the conversion.
 
+General data format (.gdf)
+==========================
+
+GDF files can be read in using :func:`mne.io.read_raw_edf`.
+
+`GDF (General Data Format) <https://arxiv.org/abs/cs/0608052>`_ is a flexible
+format for biomedical signals, that overcomes some of the limitations of the
+EDF format. The original specification (GDF v1) includes a binary header,
+and uses an event table. An updated specification (GDF v2) was released in
+2011 and adds fields for additional subject-specific information (gender,
+age, etc.) and allows storing several physical units and other properties.
+Both specifications are supported in MNE.
+
 Neuroscan CNT data format (.cnt)
 ================================
 

mne/datasets/utils.py

@@ -228,7 +228,7 @@ def _data_path(path=None, force_update=False, update_path=True, download=True,
     path = _get_path(path, key, name)
     # To update the testing or misc dataset, push commits, then make a new
     # release on GitHub. Then update the "releases" variable:
-    releases = dict(testing='0.32', misc='0.3')
+    releases = dict(testing='0.33', misc='0.3')
     # And also update the "hashes['testing']" variable below.
 
     # To update any other dataset, update the data archive itself (upload
@@ -285,7 +285,7 @@ def _data_path(path=None, force_update=False, update_path=True, download=True,
         sample='1d5da3a809fded1ef5734444ab5bf857',
         somato='f3e3a8441477bb5bacae1d0c6e0964fb',
         spm='f61041e3f3f2ba0def8a2ca71592cc41',
-        testing='bcda2bb49dfa8a9400aaeeb3c4b0a072',
+        testing='37e965395f04ed357605e796fde104f3',
         multimodal='26ec847ae9ab80f58f204d09e2c08367',
         visual_92_categories='46c7e590f4a48596441ce001595d5e58',
         mtrf='273a390ebbc48da2c3184b01a82e4636',