def display_viewer_syntax(files,
colormaps=[],
minmax=[],
opacities=[],
mode='',
verbose=1):
"""
Print the syntax to open a viewer and display images for QC. To use default values, enter empty string: ''
Parameters
----------
files [list:string]: list of NIFTI file names
colormaps [list:string]: list of colormaps associated with each file. Available colour maps: see dict_fsleyes
minmax [list:string]: list of min,max brightness scale associated with each file. Separate with comma.
opacities [list:string]: list of opacity associated with each file. Between 0 and 1.
Returns
-------
None
Example
-------
sct.display_viewer_syntax([file1, file2, file3])
sct.display_viewer_syntax([file1, file2], colormaps=['gray', 'red'], minmax=['', '0,1'], opacities=['', '0.7'])
"""
list_viewer = ['fsleyes', 'fslview_deprecated',
'fslview'] # list of known viewers. Can add more.
dict_fslview = {
'gray': 'Greyscale',
'red-yellow': 'Red-Yellow',
'blue-lightblue': 'Blue-Lightblue',
'red': 'Red',
'green': 'Green',
'random': 'Random-Rainbow',
'hsv': 'hsv',
'subcortical': 'MGH-Subcortical'
}
dict_fsleyes = {
'gray': 'greyscale',
'red-yellow': 'red-yellow',
'blue-lightblue': 'blue-lightblue',
'red': 'red',
'green': 'green',
'random': 'random',
'hsv': 'hsv',
'subcortical': 'subcortical'
}
selected_viewer = None
# find viewer
exe_viewers = [viewer for viewer in list_viewer if check_exe(viewer)]
if exe_viewers:
selected_viewer = exe_viewers[0]
else:
return
# loop across files and build syntax
cmd = selected_viewer
# add mode (only supported by fslview for the moment)
if mode and selected_viewer in ['fslview', 'fslview_deprecated']:
cmd += ' -m ' + mode
for i in range(len(files)):
# add viewer-specific options
if selected_viewer in ['fslview', 'fslview_deprecated']:
cmd += ' ' + files[i]
if colormaps:
if colormaps[i]:
cmd += ' -l ' + dict_fslview[colormaps[i]]
if minmax:
if minmax[i]:
cmd += ' -b ' + minmax[i] # a,b
if opacities:
if opacities[i]:
cmd += ' -t ' + opacities[i]
if selected_viewer in ['fsleyes']:
cmd += ' ' + files[i]
if colormaps:
if colormaps[i]:
cmd += ' -cm ' + dict_fsleyes[colormaps[i]]
if minmax:
if minmax[i]:
cmd += ' -dr ' + ' '.join(minmax[i].split(',')) # a b
if opacities:
if opacities[i]:
cmd += ' -a ' + str(
float(opacities[i]) * 100) # in percentage
cmd += ' &'
# display
if verbose:
printv('\nDone! To view results, type:')
printv(cmd + '\n', verbose=1, type='info')
def display_viewer_syntax(files, colormaps=[], minmax=[], opacities=[], mode='', verbose=1):
"""
Print the syntax to open a viewer and display images for QC. To use default values, enter empty string: ''
Parameters
----------
files [list:string]: list of NIFTI file names
colormaps [list:string]: list of colormaps associated with each file. Available colour maps: see dict_fsleyes
minmax [list:string]: list of min,max brightness scale associated with each file. Separate with comma.
opacities [list:string]: list of opacity associated with each file. Between 0 and 1.
Returns
-------
None
Example
-------
sct.display_viewer_syntax([file1, file2, file3])
sct.display_viewer_syntax([file1, file2], colormaps=['gray', 'red'], minmax=['', '0,1'], opacities=['', '0.7'])
"""
list_viewer = ['fsleyes', 'fslview_deprecated', 'fslview'] # list of known viewers. Can add more.
dict_fslview = {'gray': 'Greyscale', 'red-yellow': 'Red-Yellow', 'blue-lightblue': 'Blue-Lightblue', 'red': 'Red',
'green': 'Green', 'random': 'Random-Rainbow', 'hsv': 'hsv', 'subcortical': 'MGH-Subcortical'}
dict_fsleyes = {'gray': 'greyscale', 'red-yellow': 'red-yellow', 'blue-lightblue': 'blue-lightblue', 'red': 'red',
'green': 'green', 'random': 'random', 'hsv': 'hsv', 'subcortical': 'subcortical'}
selected_viewer = None
# find viewer
exe_viewers = [viewer for viewer in list_viewer if check_exe(viewer)]
if exe_viewers:
selected_viewer = exe_viewers[0]
else:
return
# loop across files and build syntax
cmd = selected_viewer
# add mode (only supported by fslview for the moment)
if mode and selected_viewer in ['fslview', 'fslview_deprecated']:
cmd += ' -m ' + mode
for i in range(len(files)):
# add viewer-specific options
if selected_viewer in ['fslview', 'fslview_deprecated']:
cmd += ' ' + files[i]
if colormaps:
if colormaps[i]:
cmd += ' -l ' + dict_fslview[colormaps[i]]
if minmax:
if minmax[i]:
cmd += ' -b ' + minmax[i] # a,b
if opacities:
if opacities[i]:
cmd += ' -t ' + opacities[i]
if selected_viewer in ['fsleyes']:
cmd += ' ' + files[i]
if colormaps:
if colormaps[i]:
cmd += ' -cm ' + dict_fsleyes[colormaps[i]]
if minmax:
if minmax[i]:
cmd += ' -dr ' + ' '.join(minmax[i].split(',')) # a b
if opacities:
if opacities[i]:
cmd += ' -a ' + str(float(opacities[i]) * 100) # in percentage
cmd += ' &'
# display
if verbose:
printv('\nDone! To view results, type:')
printv(cmd + '\n', verbose=1, type='info')