-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathREADME
136 lines (78 loc) · 3.15 KB
/
README
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
h5browse (formerly dataviz) is a utility for browsing HDF5 files.
It was developed for analyzing neuronal simulation data saved in a
custom format. But the interface is generic enough to display simple
HDF5 files. The tools are totally for neuronal data analysis. But the
plan is to make it a more general tool.
As of 2015-12-21, it supports displaying the tree structure of an HDF5
file, node attributes and dataset contents. You can select arbitrary
fields in a dataset for displaying X-Y plots.
Implementation of editing HDF5 is incomplete.
Note that being based on h5py library it inherits the limitations of
the same.
This is a rewrite of the old code. Replaced PyQwt with
PyQtGraph. Written from scratch in Python 3. Compatible with Python2.7.
Installation
============
Requirements
------------
numpy, h5py, PyQtGraph.
As of Fri, Aug 21, 2015 only PyQtGraph devel branch on github supports
PyQt5. Install it using:
git clone -b develop https://github.com/pyqtgraph/pyqtgraph.git
cd pyqtgraph
python setup.py install
You also need setuptools to use setup.py for standard installation.
Simpler if you have pip:
pip install git+https://github.com/pyqtgraph/pyqtgraph.git@develop
or faster:
pip install https://github.com/pyqtgraph/pyqtgraph/archive/develop.zip
Install
-------
Install from PyPI:
pip install h5browse
You can also download the sourcecode and run the h5browse.py file
using python.
git clone https://github.com/subhacom/h5browse.git
python h5browse/h5browse/h5browse.py
Troubleshooting
===============
* Problem with Anaconda(Python3) on Windows 7 and PyQt5:
This application failed to start because it could not find or load the
Qt platform plugin "windows".
Solution:
From: https://groups.google.com/a/continuum.io/forum/#!topic/anaconda/xgDvOCbOXkI
Create a PyQt5 environment:
conda create -n pyqt5 python
Then activate the PyQt5 environment (skip `source` on anaconda command
prompt on Windows):
source activate pyqt5
* Problem with files generated by PyTables (pandas, and any other
software that relies on PyTables for writing HDF5). Particularly,
the system attributes like CLASS, TITLE etc. remain empty and you
see exceptions in the console:
IOError: Empty attributes cannot be read
- The issue is: https://github.com/h5py/h5py/issues/279
or
IOError: Unable to read attribute (No appropriate function for conversion path)
The issue is: https://github.com/h5py/h5py/issues/585
These should be resolved once h5py is fixed/enhanced.
TODO
====
Important features to port from old code:
Filtering
Selection by regular expression
Python shell
Not handling in near future
---------------------------
Nested datasets. Datasets with entries that are variable length
arrays.
Images? Need to have a look at existing standards.
Other software
==============
h5browse is aimed at reading HDF5 files.
If you want fine control over plotting, a possible candidate is veusz.
If you want to edit HDF5 files, hdfview is the standard graphical tool
for that.
--------------------
Author: Subhasis Ray
email: lastname dot firstname at gmail dot com