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18.0 9.0 26.0 6.02 MB

Python library for NIX

Home Page: https://readthedocs.org/projects/nixpy

License: Other

Python 93.93% C++ 6.07%

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nixpy's Issues

Problem during batch operations

@Drumstick12 pointed me to an issue related with batch operations on multiple files.

Consider the following code:

import nix
import numpy as np
import glob

def create_files(count):
    for i in range(count):
        f = nix.File.open("test_"+str(i)+".h5", nix.FileMode.Overwrite)
        b = f.create_block("test_block_" + str(i), "test")
        da = b.create_data_array("array", "test", data=np.random.rand(1000))
        da.append_sampled_dimension(1.)
        da.unit = "mV"
        da.label = "voltage"
        f.close()
        da = None  # this is essential; code fails, otherwise
        b =  None  # do

def reload_files():
    files = glob.glob('test*.h5')
    for fi in files:
        f = nix.File.open(fi, nix.FileMode.ReadOnly)
        b = f.blocks[0]
        da = b.data_arrays['array']
        data = da[:]
        da = None  # this is essential
        b = None  # do 
        f.close()

if __name__ == "__main__":
    create_files(10)
    reload_files()

It creates a few files, stores some data and subsequently re-opens them to read the data. Without setting the variables for the block and the data array explicitly to None the code fails with the same H5Lexists: not a location exception.

Setting everything to None, is ok for a few variables, but is really annoying if you open a lot of entities.

setup.py uses module commands

The module commands is deprecated since python 2.6 and not available on python 3. Should be replaced by module subprocess.

See: https://docs.python.org/2/library/commands.html

nixpy build fails

... due to the latest changes in the Nix library. In particular the pySection.createProperty fails.

DataType not understood error in Property handling

The following snippets (kind of) work but produce Type errors I do not understand:

import nix
f = nix.File.open('test.h5', nix.FileMode.Overwrite)
s = f.create_section('test','test')

# the following code works fine, even if data types do not match
p = s.create_property('test_p', nix.DataType.Int32)
p.data_type
     nix.core.DataType.Int32
p.values = [nix.Value(1)]
p.data_type
     nix.core.DataType.Int64

# here it crashes:

p2 = s.create_property('test_p2', nix.Value(1))
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
TypeError: data type not understood

# funny enough p2 exists, has the correct data type and value
p2.data_type
     nix.core.DataType.Int64
p2.values
     (Value{[DataType::Int64] 1},)

Create mixin for EntityWithSources

Subclass ProxyList and add an append method

Write a mixin that paches all subclasses of EntityWithSources:

The mixin should define a property sources using the above mentioned proxy
Write a unit test

getProperties()

Currently the properties of a section can only be listed by _properties. It might be usefull to "really" expose them by a proper method (or by removing the underscore).

Inherited properties for Section

Section should have a property inherited_properties that works like properties but without delete that provides access to all inherited properties.

Metadata dict access or "value unpacking is a joke currently"

Give a section s and a property called "Type" that has a value (type str) of "calcium imaging" this is how you currently get to it:

v = s['Type'].values[0].value
print(v)
# 'calcium imaging'

I would suggest that we add another way, so we have two ways of getting to properties via dict-like-access: 1) s['key'] and 2) s.props['key']. One of them (I think the latter) should give you the actual nix.Property while the other should apply magic[1] to directly give you back the "unpacked" value (or list of values), i.e.:

v = s['key']
print(v)
#1.0 or "str" or [1.0, 2.0, 3.0]

p = s.props['key']
print(p)
Property: {name = Type}

This is python after all. What do you guys think?

[1] with magic I mean logic

Section: dict-like section creation

On the mission to make working with metadata as close to dicts (and pythonic) as possible there is not that much missing. For the object creation, the properties side of things has been solved with pr #101. The thing that remains is creation of sections, currently done via section.create_section('name', 'type')
Following ideas came to my mind:
Create section via __setitem__ and a tuple, i.e. s['new section'] = ('type'). If people fear that this is too confusing to value creation (which is done via lists, i.e. s['prop'] = [1, 2, 3]) then maybe we could introduce a dummy class (e.g. a collections.namedtuple) with a short name (nix.S): s['new section'] = nix.S('type').
I think I personally prefer the first version, i.e. the tuple based approach.

Use tuple instead of list

We should evaluate whether it would be more consistent to use tuple instead of list for properties of the python bindings that correspond to std::vector in the c++ library. This is of course only relevant for cases where we do not use ListProxy.

Examples:

SimpleTag.units
SimpleTag.position
SimpleTag.extent

A maybe possible solution would be to change vector_transmogrify to convert to tuple instead of list.

Typo in DataArrat::create_reange_dimension

setup.py: NIXINC_DIR, NIXLIB_DIR are not honoured anymore

Numpy support for DataArray

Improve data access for the DataArray and add support for reading and writing numpy arrays.
Would be nice if slicing and writing would work like in h5py.

Add tutorial and install instruction to documentation

There still some TODOs in the sphinx documentation. Remove them and replace them with nice text.

bindings for util and data access methods needed

Prepare alpha release

This is a list of steps for the alpha release: maybe it would be a good idea to write a shell script that does the version changes, tagging and uploading automatically and add it to the repository (one for nix and one for nixpy).

Create a debian branch with all information needed for a debian package
Synchronize version number with nix version number
Tag nixpy and nix with the respective version
Upload package to PyPi (postponed due to name conflict see #49 )
Upload the nix and nixpy debian package to lauchpad
Upload the nix and nixpy doc to gh-pages

cannot import freshly build library

OS: OS-X

When trying to import nixpy:

ImportError: dlopen(nix/core.so, 2): Symbol not found: __ZN3nixlsERNSt3__113basic_ostreamIcNS0_11char_traitsIcEEEERKNS_9SimpleTagE
  Referenced from: nix/core.so
  Expected in: flat namespace
 in nix/core.so

Bindings for DataTag

Add bindings for DataTag:

Use a mixin if necessary
Make sure the mixin for EntityWithSources patches DataTag
Write a unit test

Tutorial

Exposing the new C++ classes and completion of bindings for Tag and MultiTag

The ZonedIO needs to be exposed in python.
We added the retrieveReference and retrieveFeatureData methods to Tags, these need to added to the bindings.

At the moment, nixpy does not work with a current build of the nix library

has_property_by_name takes longer when invoked via block.metadata

The fellowing code:

nix_file = nix.File.open('/home/garbers/foo.h5', nix.FileMode.ReadOnly)

profile.run('nix_file.blocks[0].metadata.has_property_by_name(\'Genotype\')')
profile.run('nix_file.sections[0].has_property_by_name(\'Genotype\')')
print nix_file.blocks[0].metadata == nix_file.sections[0]

nix_file.close()

leads to this output:

15 function calls in 0.120 seconds

Ordered by: standard name

ncalls tottime percall cumtime percall filename:lineno(function)
4 0.000 0.000 0.000 0.000 :0(getattr)
1 0.000 0.000 0.000 0.000 :0(hasattr)
2 0.000 0.000 0.000 0.000 :0(isinstance)
1 0.000 0.000 0.000 0.000 :0(setattr)
1 0.000 0.000 0.000 0.000 :0(setprofile)
1 0.120 0.120 0.120 0.120 :1()
1 0.000 0.000 0.000 0.000 file.py:20(init)
1 0.000 0.000 0.000 0.000 file.py:37(blocks)
1 0.000 0.000 0.120 0.120 profile:0(nix_file.blocks[0].metadata.has_property_by_name('Genotype'))
0 0.000 0.000 profile:0(profiler)
1 0.000 0.000 0.000 0.000 proxy_list.py:18(init)
1 0.000 0.000 0.000 0.000 proxy_list.py:27(getitem)

15 function calls in 0.000 seconds

Ordered by: standard name

ncalls tottime percall cumtime percall filename:lineno(function)
4 0.000 0.000 0.000 0.000 :0(getattr)
1 0.000 0.000 0.000 0.000 :0(hasattr)
2 0.000 0.000 0.000 0.000 :0(isinstance)
1 0.000 0.000 0.000 0.000 :0(setattr)
1 0.000 0.000 0.000 0.000 :0(setprofile)
1 0.000 0.000 0.000 0.000 :1()
1 0.000 0.000 0.000 0.000 file.py:27(init)
1 0.000 0.000 0.000 0.000 file.py:71(sections)
1 0.000 0.000 0.000 0.000 profile:0(nix_file.sections[0].has_property_by_name('Genotype'))
0 0.000 0.000 profile:0(profiler)
1 0.000 0.000 0.000 0.000 proxy_list.py:18(init)
1 0.000 0.000 0.000 0.000 proxy_list.py:27(getitem)
True

For some reason the call to "has_property_by_name" seems to take (way) longer when invoked through the Blocks metadata compared to being invoked on the same section directly. This issue seems to be dependent on the amount of sections present in the file as it those only "apear" for files with quite a lot of sections (therefore i do not link to foo.h5 here as it is ~150mb; you can find it on gate.g-node under /groups/wachtler/share)

Transmorgification for nix entities

I suggest that we map our nix entities to None if they are not initialized.

Add docstrings and generate sphinx documentation

Add docstrings for all methods and properties written in python or added via bindings.

C++11 has multi-line string literals, which could be useful for that purpose.

I suggest we use the sphinxy (http://sphinx-doc.org/domains.html#info-field-lists) style for field list descriptions:

def foo(bar, bla):
    """
    This does some nice foo.

    :param str bar: Your favorite bar
    :param int bla: Number of words per second

    :return: A suitable foo bar.
    :rtype: Bar
    """
    pass

Inconsistencies between the index while indexing and creating of dimension

Enable use of numpy types

Implement transmorgify for DataType to numpy type:

from python: accept everything that PyArray_DescrConverter accepts plus DataType
to python: convert always to numpy dtype

Bindings for SimpleTag and Feature

Add bindings for SimpleTag and Feature:

Use a mixin if necessary
Make sure the mixin for EntityWithSources patches SimpleTag
Write a unit test

Installation

Find method with filter for sources

Block and Source should have a find method for sources that works similar to the one on the c++ lib.

Bindings for validation methods

Create bindings for file validation

can't set label of dimension

Trying to set the label of a sampled dimension like this fails:

sd = video_data.append_sampled_dimension(1.0)
sd.label("width")

TypeError: 'NoneType' object is not callable

edit: The same applies to unit of range dimension

multi_tag retrieves incorrect data

Dear Nix Developer Team

I was trying to use multi_tag.retrieve_data(). it retrieves wrong data.
Here is the test code.

import nix
import numpy as np
from math import pi as PI
import os
from matplotlib import pyplot as plt




sig1 = np.arange(2, 20)


fle = 'test.h5'

if os.path.isfile(os.path.join(os.getcwd(), fle)):
  os.remove(fle)

nixFile = nix.File.open(fle, nix.FileMode.Overwrite)
blk = nixFile.create_block('blk1', 'testBlock')
da1 = blk.create_data_array('sig1', 'test',  data=sig1)
dim = da1.append_sampled_dimension(0.1)
dim.unit = 's'
dim.offset = 0.2

pos = blk.create_data_array('pos1', 'test', data=[0.4, 0.8, 1.2])
pos.append_set_dimension()
pos.append_set_dimension()

ext = blk.create_data_array('ext1', 'test', data=[0.2, 0.2, 0.2])
ext.append_set_dimension()
ext.append_set_dimension()

tag1 = blk.create_multi_tag('tag1', 'test', pos)
tag1.extents = ext

tag1.references.append(da1)


snips = [tag1.retrieve_data(p, 0)[:] for p in range(3)]
print(snips)

The expected output here is
[array([4, 5]), array([8, 9]), array([12, 13])]
whereas the output is
[array([6, 7]), array([10, 11]), array([14, 15])]

It seems that the offset hasn't been taken into account.
Please have a look.

Cheers
Ajay

License must be changed to e.g. BSD-3

echoing G-Node/nix#542

PyPi name conflict

There is a conflicting package with the name nix on PyPi. This conflict has to be resolved.

Set PyPi package name to nixpy
Set base package name to nixpy?
Prepare repo for package upload

Overload for create_data_array

Implement an overload for create_data_array equivalent to the old create_data method.

The method create_data_array should either accept a numpy array or type and size.

[build] OSX link error due: wanting to link -lboost_python-py27

Probably introduced by commit 83e70c2. On OSX, with homebrew it seems the py2 boost python library is still called libboost_python.dylib.

Ability to store large strings (eg. log data etc.)

Is there a way to properly do this ATM.

tag.retrieve_data gives Segmentation Fault

Dear Nix Developer team

I tried to use tag.retrieve_data and got a Segmentation Fault . Here is the test code

import nix
import numpy as np
from math import pi as PI
import os
from matplotlib import pyplot as plt



fs = 1000.0
t = np.arange(0, 10, 1 / fs)
sig1 = np.random.rand(t.shape[0])
sig2 = np.sin(2 * PI * 0.5 * t)

fle = 'test.h5'

if os.path.isfile(os.path.join(os.getcwd(), fle)):
  os.remove(fle)

nixFile = nix.File.open(fle, nix.FileMode.Overwrite)
blk = nixFile.create_block('blk1', 'testBlock')
da1 = blk.create_data_array('sig1', 'test',  data=sig1)
dim = da1.append_sampled_dimension(1 / fs)
dim.unit = 's'
da2 = blk.create_data_array('sig2', 'test', data=sig2)
dim = da2.append_sampled_dimension(1 / fs)
dim.unit = 's'

tag1 = blk.create_tag('tag1', 'test', [2])
tag1.extent = [0.5]

tag1.references.append(da1)
tag1.references.append(da2)

snip1 = tag1.retrieve_data(0)
t1 = np.linspace(0, tag1.extent[0], snip1.shape[0]) + tag1.position[0]

plt.plot(t1, snip1)
plt.show()

Please help me.

Thanks
Ajay

Make properties directly accessible from the section

Properties could be accessible directly from the section, further it would be nice to access properties also by their names as it is possible in the python-odml library.

sec = ...
sec.create_property("foo")
p = sec["foo"]
# instead of sec.properties["foo"]

Test fails with newest nixpy commit

Dear Nix developer team

I tried to build nixpy and a test failed. Here are some details:

nix version installed: commit 7fd231bc753ed4974f5538b3e574c2ef1865bb92
nixpy version tried: commit 4a0e42d

Here is test output:

~/repos/nixpy$ python setup.py test
running test
running egg_info
writing nix.egg-info/PKG-INFO
writing top-level names to nix.egg-info/top_level.txt
writing dependency_links to nix.egg-info/dependency_links.txt
reading manifest file 'nix.egg-info/SOURCES.txt'
writing manifest file 'nix.egg-info/SOURCES.txt'
running build_ext
copying build/lib.linux-x86_64-2.7/nix/core.so -> nix
test_block_data_arrays (nix.test.test_block.TestBlock) ... ok
test_block_definition (nix.test.test_block.TestBlock) ... ok
test_block_eq (nix.test.test_block.TestBlock) ... ok
test_block_find_sources (nix.test.test_block.TestBlock) ... ok
test_block_id (nix.test.test_block.TestBlock) ... ok
test_block_multi_tags (nix.test.test_block.TestBlock) ... ok
test_block_name (nix.test.test_block.TestBlock) ... ok
test_block_sources (nix.test.test_block.TestBlock) ... ok
test_block_tags (nix.test.test_block.TestBlock) ... ok
test_block_timestamps (nix.test.test_block.TestBlock) ... ok
test_block_type (nix.test.test_block.TestBlock) ... ok
test_data_array_coefficients (nix.test.test_data_array.TestDataArray) ... ok
test_data_array_data (nix.test.test_data_array.TestDataArray) ... ok
test_data_array_definition (nix.test.test_data_array.TestDataArray) ... ok
test_data_array_dimensions (nix.test.test_data_array.TestDataArray) ... ok
test_data_array_dtype (nix.test.test_data_array.TestDataArray) ... ok
test_data_array_eq (nix.test.test_data_array.TestDataArray) ... ok
test_data_array_exp_origin (nix.test.test_data_array.TestDataArray) ... ok
test_data_array_id (nix.test.test_data_array.TestDataArray) ... ok
test_data_array_label (nix.test.test_data_array.TestDataArray) ... ok
test_data_array_name (nix.test.test_data_array.TestDataArray) ... ok
test_data_array_sources (nix.test.test_data_array.TestDataArray) ... ok
test_data_array_timestamps (nix.test.test_data_array.TestDataArray) ... ok
test_data_array_type (nix.test.test_data_array.TestDataArray) ... ok
test_data_array_unit (nix.test.test_data_array.TestDataArray) ... ok
test_range_dimension (nix.test.test_dimensions.TestDimensions) ... FAIL
test_sample_dimension (nix.test.test_dimensions.TestDimensions) ... ok
test_set_dimension (nix.test.test_dimensions.TestDimensions) ... ok
test_feature_data (nix.test.test_feature.TestFeature) ... ok
test_feature_eq (nix.test.test_feature.TestFeature) ... ok
test_feature_id (nix.test.test_feature.TestFeature) ... ok
test_feature_link_type (nix.test.test_feature.TestFeature) ... ok
test_file_blocks (nix.test.test_file.TestFile) ... ok
test_file_find_sections (nix.test.test_file.TestFile) ... ok
test_file_format (nix.test.test_file.TestFile) ... ok
test_file_sections (nix.test.test_file.TestFile) ... ok
test_file_timestamps (nix.test.test_file.TestFile) ... ok
test_multi_tag_definition (nix.test.test_multi_tag.TestMultiTag) ... ok
test_multi_tag_eq (nix.test.test_multi_tag.TestMultiTag) ... ok
test_multi_tag_extents (nix.test.test_multi_tag.TestMultiTag) ... ok
test_multi_tag_feature_data (nix.test.test_multi_tag.TestMultiTag) ... ok
test_multi_tag_features (nix.test.test_multi_tag.TestMultiTag) ... ok
test_multi_tag_id (nix.test.test_multi_tag.TestMultiTag) ... ok
test_multi_tag_name (nix.test.test_multi_tag.TestMultiTag) ... ok
test_multi_tag_positions (nix.test.test_multi_tag.TestMultiTag) ... ok
test_multi_tag_references (nix.test.test_multi_tag.TestMultiTag) ... ok
test_multi_tag_retrieve_data (nix.test.test_multi_tag.TestMultiTag) ... ok
test_multi_tag_timestamps (nix.test.test_multi_tag.TestMultiTag) ... ok
test_multi_tag_type (nix.test.test_multi_tag.TestMultiTag) ... ok
test_multi_tag_units (nix.test.test_multi_tag.TestMultiTag) ... ok
test_property_definition (nix.test.test_property.TestProperty) ... ok
test_property_eq (nix.test.test_property.TestProperty) ... ok
test_property_id (nix.test.test_property.TestProperty) ... ok
test_property_mapping (nix.test.test_property.TestProperty) ... ok
test_property_name (nix.test.test_property.TestProperty) ... ok
test_property_values (nix.test.test_property.TestProperty) ... ok
test_value_attrs (nix.test.test_property.TestValue) ... ok
test_value_bool (nix.test.test_property.TestValue) ... ok
test_value_float (nix.test.test_property.TestValue) ... ok
test_value_int (nix.test.test_property.TestValue) ... ok
test_value_str (nix.test.test_property.TestValue) ... ok
test_proxy_list_contains (nix.test.test_proxy_list.TestProxyList) ... ok
test_proxy_list_delitem (nix.test.test_proxy_list.TestProxyList) ... ok
test_proxy_list_getitem (nix.test.test_proxy_list.TestProxyList) ... ok
test_proxy_list_iterators (nix.test.test_proxy_list.TestProxyList) ... ok
test_proxy_list_len (nix.test.test_proxy_list.TestProxyList) ... ok
test_proxy_list_str (nix.test.test_proxy_list.TestProxyList) ... ok
test_section_definition (nix.test.test_section.TestSection) ... ok
test_section_eq (nix.test.test_section.TestSection) ... ok
test_section_find_sections (nix.test.test_section.TestSection) ... ok
test_section_id (nix.test.test_section.TestSection) ... ok
test_section_mapping (nix.test.test_section.TestSection) ... ok
test_section_name (nix.test.test_section.TestSection) ... ok
test_section_properties (nix.test.test_section.TestSection) ... ok
test_section_repository (nix.test.test_section.TestSection) ... ok
test_section_sections (nix.test.test_section.TestSection) ... ok
test_section_type (nix.test.test_section.TestSection) ... ok
test_source_definition (nix.test.test_source.TestSource) ... ok
test_source_eq (nix.test.test_source.TestSource) ... ok
test_source_find_sources (nix.test.test_source.TestSource) ... ok
test_source_id (nix.test.test_source.TestSource) ... ok
test_source_name (nix.test.test_source.TestSource) ... ok
test_source_sources (nix.test.test_source.TestSource) ... ok
test_source_timestamps (nix.test.test_source.TestSource) ... ok
test_source_type (nix.test.test_source.TestSource) ... ok
test_sources_extend (nix.test.test_source.TestSource) ... ok
test_tag_definition (nix.test.test_tag.TestTag) ... ok
test_tag_eq (nix.test.test_tag.TestTag) ... ok
test_tag_extent (nix.test.test_tag.TestTag) ... ok
test_tag_features (nix.test.test_tag.TestTag) ... ok
test_tag_id (nix.test.test_tag.TestTag) ... ok
test_tag_name (nix.test.test_tag.TestTag) ... ok
test_tag_position (nix.test.test_tag.TestTag) ... ok
test_tag_references (nix.test.test_tag.TestTag) ... ok
test_tag_retrieve_feature_data (nix.test.test_tag.TestTag) ... ok
test_tag_timestamps (nix.test.test_tag.TestTag) ... ok
test_tag_type (nix.test.test_tag.TestTag) ... ok
test_tag_units (nix.test.test_tag.TestTag) ... ok
test_name_check (nix.test.test_util.TestUtil) ... ok
test_name_sanitizer (nix.test.test_util.TestUtil) ... ok
test_unit_is_atomic (nix.test.test_util.TestUtil) ... ok
test_unit_is_compound (nix.test.test_util.TestUtil) ... ok
test_unit_is_si (nix.test.test_util.TestUtil) ... ok
test_unit_sanitizer (nix.test.test_util.TestUtil) ... ok
test_unit_scalable (nix.test.test_util.TestUtil) ... ok
test_unit_scaling (nix.test.test_util.TestUtil) ... ok
test_unit_split (nix.test.test_util.TestUtil) ... ok
test_unit_split_compound (nix.test.test_util.TestUtil) ... ok

======================================================================
FAIL: test_range_dimension (nix.test.test_dimensions.TestDimensions)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/ajay/repos/nixpy/nix/test/test_dimensions.py", line 104, in test_range_dimension
    assert(self.range_dim.index_of(10.) == (round(10./3.14)))
AssertionError

----------------------------------------------------------------------
Ran 108 tests in 1.113s

FAILED (failures=1)

Please have a look

Thanks
Ajay

unicode string handling

We currently cannot handle unicode arguments, e.g.:

   da = self._create_data_array(name, array_type, dtype, shape)
Boost.Python.ArgumentError: Python argument types in
    Block._create_data_array(Block, unicode, str, numpy.dtype, tuple)
did not match C++ signature:
_create_data_array(nix::Block {lvalue}, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, nix::DataType, nix::NDSizeBase<unsigned long long>)

get_sections_by_value, get_blocks_by_value

Id like to suggest methods which receive a value and return all sections/blocks/data_arrays that contain that value. Something like:

def get_sections_by_value(value, nix_file):
    return nix_file.find_sections(lambda x:any([any([value in i for i in 
                                                       e.values]) for e in 
                                                       x._properties]))

def get_blocks_by_value(value, nix_file):
    return filter(lambda x:len(get_sections_by_value(value, x.metadata))>0, 
                  nix_file.blocks)

but with all the corner cases and type issues solved and of course, well not in python. I think "give me all recordings in which i wrote something like whatever" is quite a usual use case. (Yes i know that this is most probaly non trivial)

NIX changes: Block::create_data_array changes

We broke nixpy

Writing of data via index+slices silently ignores data exceeding the DataArray's shape

Look here:

import nix
fd = nix.File.open('test.h5', nix.FileMode.Overwrite)
b = fd.create_block('b', 'notype')
d = b.create_data_array('da', 'stillnotype')
d = b.create_data_array('da', 'stillnotype', nix.DataType.Double, (0,0))
d[:, :] = np.ones((23, 42))
d[...]
# Out: array([], shape=(0, 0), dtype=float64)
d2 = b.create_data_array('da', 'stillnotype', nix.DataType.Double, (12,13))
d2 = b.create_data_array('da2', 'stillnotype', nix.DataType.Double, (12,13))
d2[:, :] = np.ones((23, 42))
d2[...]
d2.shape
# Out: (12, 13)

Find method with filter for sections

Block and Section should have a find method for sections that works similar to the one on the c++ lib.

unidentified C++ exception when reassigning entities to variables

I came across this error, when I looped over several files, extracted data_arrays from them, and assigned them to the same variable.

Setting them to None solved the problem.

HDF5-DIAG: Error detected in HDF5 (1.8.11) thread 139774801626944:
  #000: ../../../src/H5A.c line 2589 in H5Aexists(): not a location
    major: Invalid arguments to routine
    minor: Inappropriate type
  #001: ../../../src/H5Gloc.c line 195 in H5G_loc(): invalid group ID
    major: Invalid arguments to routine
    minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.11) thread 139774801626944:
  #000: ../../../src/H5A.c line 2589 in H5Aexists(): not a location
    major: Invalid arguments to routine
    minor: Inappropriate type
  #001: ../../../src/H5Gloc.c line 195 in H5G_loc(): invalid group ID
    major: Invalid arguments to routine
    minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.11) thread 139774801626944:
  #000: ../../../src/H5A.c line 551 in H5Aopen(): not a location
    major: Invalid arguments to routine
    minor: Inappropriate type
  #001: ../../../src/H5Gloc.c line 195 in H5G_loc(): invalid group ID
    major: Invalid arguments to routine
    minor: Bad value
Traceback (most recent call last):
  File "detect_peak_troughs_hdf5.py", line 47, in <module>
    print trough_array
RuntimeError: unidentifiable C++ exception

createMultiTag with a Duplicate name sometimes gives empty RuntimeError:

Dear Nix Developer team

When trying to create a multitag with a name that already exists in the parent block, sometimes I get

 RuntimeError: Duplicate name given - names have to be unique for a given entity type & parent. (createMultiTag)

and some other times:

 RuntimeError:

Please have a look and fix this.

Thanks
Ajay

unidentified C++ exception when opening file twice in Overwrite mode

nix_file = nix.File.open('foo.h5', nix.FileMode.Overwrite)
nix_file = nix.File.open('foo.h5', nix.FileMode.Overwrite)

Does not happen with ReadWrite or ReadOnly. But happens with combination of the Read* and Overwrite.

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