RepositoryCurrent collected state Current
Observed since 21 Oct, 09:37 UTC
No superseded metadata states collected. Unchanged observations do not create new revisions.
PACKAGE EXPLORERView in registry
ahds
PyPIPython package to parse and provide access to headers and data streams in Amira (R) files
Versions collected1
Direct dependencies2From release 0.2.4
Last observed21 Oct, 09:37 UTC
README
Version 0.2.4 documentation==============================================
``ahds``
==============================================
.. image:: https://img.shields.io/pypi/v/ahds
:alt: PyPI
.. image:: https://img.shields.io/pypi/pyversions/ahds
:alt: PyPI - Python Version
.. image:: https://travis-ci.org/emdb-empiar/ahds.svg?branch=master
:target: https://travis-ci.org/emdb-empiar/ahds
.. image:: https://readthedocs.org/projects/ahds/badge/?version=latest
:target: https://ahds.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
.. image:: https://coveralls.io/repos/github/emdb-empiar/ahds/badge.svg
:target: https://coveralls.io/github/emdb-empiar/ahds
.. contents::
----------------------------------------------
Overview
----------------------------------------------
``ahds`` is a Python package to parse and handle Amira (R) files.
It was developed to facilitate reading of Amira (R) files as part of the `EMDB-SFF toolkit <https://sfftk.readthedocs.io>`_.
.. note::
Amira (R) is a trademark of Thermo Fisher Scientific. This package is in no way affiliated with with Thermo Fisher Scientific.
----------------------------------------------
License
----------------------------------------------
``ahds`` is free software and is provided under the terms of the Apache License, Version 2.0.
::
Copyright 2017 EMBL - European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing,
software distributed under the License is distributed on an
"AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND,
either express or implied. See the License for the specific
language governing permissions and limitations under the License.
----------------------------------------
Use Cases
----------------------------------------
* Detect and parse Amira (R) headers and return structured data
* Decode data (``HxRLEByte``, ``HxZip``)
* Easy extensibility to handle previously unencountered data streams
``ahds`` was written and is maintained by Paul K. Korir but there is
`a list of contributors <https://github.com/emdb-empiar/ahds/blob/dev/CONTRIBUTORS.txt>`_.
Feel free to join this initiative.
--------------------------------------------
Installation
--------------------------------------------
``ahds`` works with Python 2.7, 3.5, 3.6 and 3.7. It requires ``numpy`` to build.
::
pip install numpy
Afterwards you may run
::
pip install ahds
.. note::
Figure out a way to avoid the need for ``numpy`` as part of the build.
--------------------------------------------
Getting Started
--------------------------------------------
You can begin playing with ``ahds`` out of the box using the provided console command ``ahds``.
.. code:: bash
me@home ~$ ahds ahds/data/FieldOnTetraMesh.am
********************************************************************************************************************************************
AMIRA (R) HEADER AND DATA STREAMS
--------------------------------------------------------------------------------------------------------------------------------------------
+-ahds/data/FieldOnTetraMesh.am AmiraFile [is_parent? True ]
| +-meta Block [is_parent? False]
| | +-file: ahds/data/FieldOnTetraMesh.am
| | +-header_length: 182
| | +-data_streams: 1
| | +-streams_loaded: False
| +-header AmiraHeader [is_parent? True ]
| | +-filetype: AmiraMesh
| | +-dimension: 3D
| | +-format: BINARY
| | +-endian: BIG
| | +-version: 2.0
| | +-extra_format: None
| | +-Parameters Block [is_parent? False]
| | +-Tetrahedra Block [is_parent? False]
| | | +-length: 23685
| +-data_streams Block [is_parent? False]
********************************************************************************************************************************************
The ``ahds`` command takes the following arguments
.. code:: bash
me@home ~$ ahds -h
usage: ahds [-h] [-s] [-d] [-l] file [file ...]
Python tool to read and display Amira files
positional arguments:
file a valid Amira file with an optional block path
optional arguments:
-h, --help show this help message and exit
-s, --load-streams whether to load data streams or not [default: False]
-d, --debug display debugging information [default: False]
-l, --literal display the literal header [default: False]
You can specify a **dotted path** after the filename to only render that the content of that field in the header:
.. code:: bash
me@home ~$ ahds ahds/data/FieldOnTetraMesh.am header
***********************************************************************************************************************************
ahds: Displaying path 'header'
-----------------------------------------------------------------------------------------------------------------------------------
+-header AmiraHeader [is_parent? True ]
| +-filetype: AmiraMesh
| +-dimension: 3D
| +-format: BINARY
| +-endian: BIG
| +-version: 2.0
| +-extra_format: None
| +-Parameters Block [is_parent? False]
| +-Tetrahedra Block [is_parent? False]
| | +-length: 23685
For debugging you can display the literal header (the exact header present in the file) using the ``-l/--literal`` flag.
Also, you can display the parsed data structure using the ``-d/--debug`` flag.
.. code:: bash
me@home ~$ ahds --literal --debug ahds/data/FieldOnTetraMesh.am
***********************************************************************************************************************************
ahds: Displaying literal header
-----------------------------------------------------------------------------------------------------------------------------------
# AmiraMesh 3D BINARY 2.0
# CreationDate: Tue Nov 2 11:46:31 2004
nTetrahedra 23685
TetrahedronData { float[3] Data } @1
Field { float[3] f } Constant(@1)
# Data section follows
***********************************************************************************************************************************
ahds: Displaying parsed header data
-----------------------------------------------------------------------------------------------------------------------------------
[{'designation': {'dimension': '3D',
'filetype': 'AmiraMesh',
'format': 'BINARY',
'version': '2.0'}},
{'comment': {'date': 'Tue Nov 2 11:46:31 2004'}},
{'array_declarations': [{'array_dimension': 23685,
'array_name': 'Tetrahedra'}]},
{'data_definitions': [{'array_reference': 'Tetrahedra',
'data_dimension': 3,
'data_index': 1,
'data_name': 'Data',
'data_type': 'float'},
{'array_reference': 'Field',
'data_dimension': 3,
'data_index': 1,
'data_name': 'f',
'data_type': 'float',
'interpolation_method': 'Constant'}]}]
********************************************************************************************************************************************
AMIRA (R) HEADER AND DATA STREAMS
--------------------------------------------------------------------------------------------------------------------------------------------
+-ahds/data/FieldOnTetraMesh.am AmiraFile [is_parent? True ]
| +-meta Block [is_parent? False]
| | +-file: ahds/data/FieldOnTetraMesh.am
| | +-header_length: 182
| | +-data_streams: 1
| | +-streams_loaded: False
| +-header AmiraHeader [is_parent? True ]
| | +-filetype: AmiraMesh
| | +-dimension: 3D
| | +-format: BINARY
| | +-endian: BIG
| | +-version: 2.0
| | +-extra_format: None
| | +-Parameters Block [is_parent? False]
| | +-Tetrahedra Block [is_parent? False]
| | | +-length: 23685
| +-data_streams Block [is_parent? False]
********************************************************************************************************************************************
By default, data streams are not read --- only the header is parsed. You may obtain the data streams using the
``-s/--load-streams`` flag.
.. code:: bash
me@home ~$ ahds --load-streams ahds/data/FieldOnTetraMesh.am
********************************************************************************************************************************************
AMIRA (R) HEADER AND DATA STREAMS
--------------------------------------------------------------------------------------------------------------------------------------------
+-ahds/data/FieldOnTetraMesh.am AmiraFile [is_parent? True ]
| +-meta Block [is_parent? False]
| | +-file: ahds/data/FieldOnTetraMesh.am
| | +-header_length: 182
| | +-data_streams: 1
| | +-streams_loaded: True
| +-header AmiraHeader [is_parent? True ]
| | +-filetype: AmiraMesh
| | +-dimension: 3D
| | +-format: BINARY
| | +-endian: BIG
| | +-version: 2.0
| | +-extra_format: None
| | +-Parameters Block [is_parent? False]
| | +-Tetrahedra Block [is_parent? False]
| | | +-length: 23685
| +-data_streams Block [is_parent? True ]
| | +-Data AmiraMeshDataStream [is_parent? False]
| | | +-data_index: 1
| | | +-dimension: 3
| | | +-type: float
| | | +-interpolation_method: None
| | | +-shape: 23685
| | | +-format: None
| | | +-data: [ 0.8917308 0.9711809 300. ],...,[ 1.4390504 1.1243758 300. ]
********************************************************************************************************************************************
----------------------------------------------
Future Plans
----------------------------------------------
* Write out valid Amira (R) files
Downloads & popularity
Awaiting observationsNo metric observations yet
Download counts and popularity will appear here as the collector receives them.
Versions 1
Collected releases| Version | Published | Direct dependencies | Open version |
|---|---|---|---|
| 0.2.4 | 4 Oct 2022 | 2 |
Package advisories
0No matching advisories collected
This describes our collected data; it is not a security assessment.
Repository
PENDINGMetadata history
Meaningful changesRecord identity
package:78c83f20852d4771900d16fd8545ca1fe4f2740a48d23ab81f3b96332dcf885e