ahds: Python package to read Amira/Avizo files

Posted 6 months, 1 week ago

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.

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. 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

Getting Started

You can begin playing with ahds out of the box using the provided console command ahds.

[email protected] ~$ 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

[email protected] ~$ 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:

[email protected] ~$ 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.

[email protected] ~$ 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.

[email protected] ~$ 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


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