''' 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)