Source code for brainvisa.tools.aimsGlobals
# -*- coding: utf-8 -*-
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"""
This module provides a few functions using pyaims (soma.aims module), and defines several lists of formats (:py:class:`neuroDiskItems.NamedFormatList`):
.. py:data:: anatomistVolumeFormats
The name of the list is *Anatomist volume formats* and it contains the volume formats which are handled by Anatomist.
.. py:data:: aimsVolumeFormats
vipVolumeFormats
The name of the list is *Aims readable volume formats* and it contains the volume formats which can be read with Aims.
.. py:data:: aimsWriteVolumeFormats
The name of the list is *Aims writable volume formats* and it contains the volume formats which can be written with Aims.
.. py:data:: aimsImageFormats
The name of the list is *Aims image formats* and it contains the 2D image formats which are readable with Aims.
.. py:data:: anatomistMeshFormats
The name of the list is *Anatomist mesh formats* and it contains the mesh formats which are handled by Anatomist.
.. py:data:: aimsMeshFormats
The name of the list is *Aims mesh formats* and it contains the mesh formats which are handled by Aims.
.. py:data:: aimsTextureFormats
The name of the list is *Aims texture formats* and it contains the texture formats which are handled by Aims.
.. py:data:: anatomistTextureFormats
The name of the list is *Anatomist texture formats* and it contains the texture formats which are handled by Anatomist.
.. py:data:: html_pdf_formats
Formats list for HTML format, and PDF if the wkhtmltopdf tool is installed on
the system and available in the PATH.
These global variables are initialized through the function :py:func:`initializeFormatLists`.
"""
from __future__ import absolute_import
import os
import string
import sys
from brainvisa.data.neuroDiskItems import createFormatList, getFormat, \
aimsFileInfo, DiskItem, Directory
from brainvisa.processes import defaultContext
from brainvisa.processing.neuroException import exceptionMessageHTML
from soma.path import find_in_path
#------------
# IMPORTANT : In a formats list, the most common formats should be placed
# at the begining of the list.
#------------
_formats_table = {
'NIFTI-1': ('gz compressed NIFTI-1 image', 'NIFTI-1 image'),
'GIS': 'GIS Image',
'SPM': 'SPM image',
'VIDA': 'VIDA Image',
'ECAT': ('ECAT v image', 'ECAT i image'),
'JPEG': 'JPEG image',
'JPEG(Qt)': 'JPEG image',
'JPG': 'JPEG image',
'GIF': 'GIF image',
'PNG': 'PNG image',
'MNG': 'MNG image',
'BMP': 'BMP image',
'PBM': 'PBM image',
'PGM': 'PGM image',
'PPM': 'PPM image',
'XBM': 'XBM image',
'XPM': 'XPM image',
'TIFF': ('TIFF image', 'TIFF(.tif) image'),
'TIFF(Qt)': ('TIFF image', 'TIFF(.tif) image'),
'MINC': ('MINC image', 'gz compressed MINC image'), # might be modified
'FREESURFER-MINC': ('FreesurferMGZ', 'FreesurferMGH'),
'DICOM': ('DICOM image', 'Directory'),
'FDF': 'FDF image',
'GIFTI': 'GIFTI file',
'MESH': 'MESH mesh',
'TRI': 'TRI mesh',
'PLY': 'PLY mesh',
'MNI_OBJ': 'MNI OBJ mesh',
#'WAVEFRONT': 'WAVEFRONT mesh',
'TEX': 'Texture',
}
_default_formats_priority = [
# volumes
'gz compressed NIFTI-1 image',
'NIFTI-1 image',
'GIS Image',
'MINC image',
'gz compressed MINC image',
'SPM image',
'Z Compressed GIS Image',
'gz Compressed GIS Image',
'ECAT v image',
'ECAT i image',
'FreesurferMGZ',
'FreesurferMGH',
'Z compressed VIDA Image',
'gz compressed VIDA Image',
'Z compressed SPM image',
'gz compressed SPM image',
'Z compressed ECAT v image',
'gz compressed ECAT v image',
'Z compressed ECAT i image',
'gz compressed ECAT i image',
'JPEG image',
'GIF image',
'PNG image',
'MNG image',
'BMP image',
'PBM image',
'PGM image',
'PPM image',
'XBM image',
'XPM image',
'TIFF image',
'TIFF(.tif) image',
'DICOM image',
'Directory', # dicom dir
'FDF image',
'VIDA Image',
# meshes
'GIFTI file',
'MESH mesh',
'TRI mesh',
'Z compressed MESH mesh',
'gz compressed MESH mesh',
'Z compressed TRI mesh',
'gz compressed TRI mesh',
'PLY mesh',
'Z compressed PLY mesh',
'gz compressed PLY mesh',
'Z compressed GIFTI file',
'gz compressed GIFTI file',
'MNI OBJ mesh',
'Z compressed MNI OBJ mesh',
'gz compressed MNI OBJ mesh',
# textures
# 'GIFTI file', # already in meshes
'Texture',
'Z compressed Texture',
'gz compressed texture',
'Z compressed GIFTI file',
'gz compressed GIFTI file',
]
[docs]def aims_to_bv_formats(formats):
'''
Translates formats (single string or list) from AIMS formats names into
BrainVISA's
'''
if isinstance(formats, (type(''), type(u''))):
formats = [formats]
oformats = []
sformats = set()
for format in formats:
f = _formats_table.get(format)
if f is not None:
if isinstance(f, (list, tuple, set)):
oformats += [x for x in f
if x not in sformats
and getFormat(x, None) is not None]
sformats.update(f)
elif f not in sformats and getFormat(f, None) is not None:
oformats.append(f)
sformats.add(f)
elif format not in sformats and getFormat(format, None) is not None:
oformats.append(format)
sformats.add(format)
return oformats
[docs]def zipped_bv_formats(formats):
'''
Translates formats (single string or list) from AIMS formats names into
BrainVISA's, and adds gz/Z compressed versions
'''
if isinstance(formats, (type(''), type(u''))):
formats = [formats]
sformats = set()
oformats = []
for format in formats:
bv_formats = aims_to_bv_formats(format)
if isinstance(bv_formats, (tuple, list, set)):
oformats += [x for x in bv_formats if x not in sformats]
sformats.update(bv_formats)
else:
bv_formats = [bv_formats]
if bv_format not in sformats:
oformats.append(bv_format)
sformats.add(bv_format)
for bv_format in bv_formats:
if bv_format.startswith('gz compressed ') \
or getFormat(bv_format).fileOrDirectory() is Directory:
continue # OK done
zf = 'gz compressed %s' % bv_format
if zf not in sformats:
oformats.append(zf)
sformats.add(zf)
zf = 'Z compressed %s' % bv_format
if zf not in sformats:
oformats.append(zf)
sformats.add(zf)
return oformats
[docs]def reordered_formats(formats, priority_list=_default_formats_priority):
'''
Reorder brainvisa formats according to a priority list: set formats from
the priority list first (in their order) when they are part of the formats
list, then append the remaining ones (in their order also)
'''
oformats = []
sformats = set(formats)
for format in priority_list:
if format in sformats and getFormat(format, None) is not None:
oformats.append(format)
done = set(oformats)
oformats += [f for f in formats
if f not in done and getFormat(f, None) is not None]
return oformats
[docs]def initializeFormatLists():
"""
Initializes several lists of formats. The lists are stored in global variables.
"""
try:
from soma import aims
# fix mgz format
aims.carto.PluginLoader.load()
io = aims.supported_io_formats() # to test is works
del io
if 'mgz' in aims.Finder.extensions('MINC'):
global _formats_table
_formats_table['MINC'] = (
'MINC image', 'gz compressed MINC image', 'FreesurferMGZ',
'FreesurferMGH')
except Exception as exc:
choice = defaultContext().ask(
exceptionMessageHTML(
(type(exc), exc, None),
afterError= '<p>AIMS could not be loaded. BrainVISA will work '
'in degraded mode, AIMS format lists will be empty and '
'processes that depend on AIMS will not load.</p>'
),
"Abort",
"Ignore",
)
if choice == 0: # in batch mode ask() returns -1 so we do not exit
sys.exit(1)
# no aims, formats lists are empty
class FakeAims(object):
@staticmethod
def supported_io_formats(*args, **kwargs):
return set()
aims = FakeAims()
global anatomistVolumeFormats
anatomistVolumeFormats = createFormatList(
'Anatomist volume formats',
reordered_formats(zipped_bv_formats(
aims.supported_io_formats('Volume', 'r'))))
global aimsVolumeFormats
aimsVolumeFormats = createFormatList(
'Aims readable volume formats',
reordered_formats(aims_to_bv_formats(
aims.supported_io_formats('Volume', 'r'))))
global aimsWriteVolumeFormats
# handle an exception for Minc/Mgz support in aims 4.6
fvolformats = aims_to_bv_formats(aims.supported_io_formats('Volume', 'w'))
if 'FreesurferMGH' in fvolformats \
and 'mgz' in aims.Finder.extensions('MINC'):
fvolformats.remove('FreesurferMGH')
fvolformats.remove('FreesurferMGZ')
aimsWriteVolumeFormats = createFormatList(
'Aims writable volume formats',
reordered_formats(fvolformats))
global aimsImageFormats
aimsImageFormats = createFormatList(
'Aims image formats',
reordered_formats((
'JPEG image',
'GIF image',
'PNG image',
'MNG image',
'BMP image',
'PBM image',
'PGM image',
'PPM image',
'XBM image',
'XPM image',
'TIFF image',
'TIFF(.tif) image',
))
)
global _aimsVolumeFormats
_aimsVolumeFormats = None
global anatomistMeshFormats
anatomistMeshFormats = createFormatList(
'Anatomist mesh formats',
reordered_formats(zipped_bv_formats(
aims.supported_io_formats('Mesh', 'r'))))
global vipVolumeFormats
vipVolumeFormats = aimsVolumeFormats
global aimsMeshFormats
aimsMeshFormats = createFormatList(
'Aims mesh formats',
reordered_formats(aims_to_bv_formats(
aims.supported_io_formats('Mesh', 'rw'))))
global aimsTextureFormats
aimsTextureFormats = createFormatList(
'Aims texture formats',
reordered_formats(aims_to_bv_formats(
aims.supported_io_formats('Texture', 'rw'))))
global anatomistTextureFormats
anatomistTextureFormats = createFormatList(
'Anatomist texture formats',
reordered_formats(zipped_bv_formats(
aims.supported_io_formats('Texture', 'r'))))
wkhtmltopdf = find_in_path('wkhtmltopdf')
if wkhtmltopdf is not None:
html_pdf_formats_l = ('HTML', 'PDF file')
else:
html_pdf_formats_l = ('HTML', )
global html_pdf_formats
html_pdf_formats = createFormatList('HTML PDF', html_pdf_formats_l)
[docs]def aimsVolumeAttributes(item, writeOnly=0, forceFormat=0):
"""
Gets the header attributes of a :py:class:`DiskItem` if the item is a readable volume.
:param item: the diskitem
:param writeonly: if True, the function just returns an empty dictionary
:param forceFormat: if True, the format of the diskitem is not checked
:returns: a dictionary containing the attributes of the header.
"""
if writeOnly:
return {}
# Get formats objects from formats names
global _aimsVolumeFormats
if _aimsVolumeFormats is None:
_aimsVolumeFormats = [getFormat(x) for x in aimsVolumeFormats] \
+ [getFormat(y) for y in ['Series of ' + x.name
for x in aimsVolumeFormats]]
result = {}
if isinstance(item, DiskItem) and \
(forceFormat or item.format in _aimsVolumeFormats) \
and item.isReadable():
result = aimsFileInfo(item.fullPath())
else:
# item is a string, use FileInfo directly
result = aimsFileInfo(item)
# Byte swapping should not be in image header but Aims gives this internal
# information.
result.pop('byte_swapping', None)
return result
# Try to open ftp connection to pelles to see if we are in shfj
import ftplib
from brainvisa.validation import ValidationError
inSHFJ = os.path.exists('/product') # and os.path.exists( '/home/appli' )
def validationOnlyInSHFJ():
if not inSHFJ:
raise ValidationError(_t_('not available outside SHFJ'))
