'''
import sys
import matplotlib.pyplot as plt
import matplotlib.image as mpimg
from jaratoolbox import histologyanalysis as ha
reload(ha)
CREATE_SVG = 0
# -- Create SVG file with images --
if CREATE_SVG:
filenameAtlas = '/var/tmp/examplesRegistration/atlas.jpg'
filenameSlice = '/var/tmp/examplesRegistration/slice.jpg'
filenameSVG = '/tmp/testfile.svg'
(atlasSize, sliceSize) = ha.save_svg_for_registration(filenameSVG, filenameAtlas, filenameSlice)
sys.exit()
# -- Transform coords --
filenameSVG = '/var/tmp/examplesRegistration/test03.svg'
(scale, translate, affine) = ha.get_svg_transform(filenameSVG)
filenameCSV = '/var/tmp/examplesRegistration/sliceCoords.csv'
coords = ha.get_coords_from_fiji_csv(filenameCSV)
newCoords = ha.apply_svg_transform(scale, translate, affine, coords)
print newCoords.T
filenameAtlas = '/var/tmp/examplesRegistration/atlas.jpg'
atlasIm = mpimg.imread(filenameAtlas)
from jaratoolbox import settings
reload(settings)
tracts = [
{'subject':'band054', 'brainArea':'LeftAC',
'recordingTract':'p1-B2-03_lateralDiI_shank4', 'atlasZ':200},
{'subject':'band054', 'brainArea':'LeftAC',
'recordingTract':'p1-B5-03_lateralDiI_shank3', 'atlasZ':208},
{'subject':'band054', 'brainArea':'LeftAC',
'recordingTract':'p1-C2-03_lateralDiI_shank2', 'atlasZ':210},
{'subject':'band054', 'brainArea':'LeftAC',
'recordingTract':'p1-C5-03_lateralDiI_shank1', 'atlasZ':217},
]
#Save svg files for registration
import pdb
HISTOLOGY_PATH = settings.HISTOLOGY_PATH
ATLAS_PATH = settings.ATLAS_PATH
for tract in tracts:
filenameAtlas = os.path.join(ATLAS_PATH,'allenCCF_Z{}.jpg'.format(tract['atlasZ']))
#pdb.set_trace()
shanksFolder = 'recordingTracts{}'.format(tract['brainArea'])
registrationFolder = 'registration{}'.format(tract['brainArea'])
filenameSlice = os.path.join(HISTOLOGY_PATH, '{}_processed'.format(tract['subject']), shanksFolder, '{}.jpg'.format(tract['recordingTract']))
filenameSVG = os.path.join(HISTOLOGY_PATH, '{}_processed'.format(tract['subject']), registrationFolder, '{}_pre.svg'.format(tract['recordingTract']))
(atlasSize, sliceSize) = ha.save_svg_for_registration(filenameSVG, filenameAtlas, filenameSlice)