#Save svg files for registration
if CASE == 0:
for sliceNum in slices:
filenameAtlas = '/mnt/jarahubdata/atlas/AllenCCF_25/JPEG/allenCCF_Z{}.jpg'.format(
ccfSlice[sliceNum])
filenameSlice = os.path.join(HISTOLOGY_DIR, subject, jpgFolder,
'{}tl.jpg'.format(sliceNum))
filenameSVG = os.path.join(HISTOLOGY_DIR, subject, registrationFolder,
'{}_pre.svg'.format(sliceNum))
(atlasSize,
sliceSize) = ha.save_svg_for_registration(filenameSVG, filenameAtlas,
filenameSlice)
#Read coords, apply transform, output counts per area
elif CASE == 1:
annotationVolume = ha.AllenAnnotation()
allSliceCounts = []
for sliceNum in slices:
filenameSVGPost = '/mnt/jarahubdata/jarashare/histology/{}/{}/{}.svg'.format(
subject, registrationFolder, sliceNum)
(scale, translate,
affine) = ha.get_svg_transform(filenameSVGPost,
sliceSize=[1388, 1040])
filenameCSV = '/mnt/jarahubdata/jarashare/histology/{}/{}/{}.csv'.format(
subject, registrationFolder, sliceNum)
coords = ha.get_coords_from_fiji_csv(filenameCSV, pixelSize=4.0048)
newCoords = ha.apply_svg_transform(scale, translate, affine, coords)
structIDs = annotationVolume.get_structure_id_many_xy(
newCoords, ccfSlice[sliceNum])
structNames = [
annotationVolume.get_structure_from_id(structID)
import os
import matplotlib.image as mpimg
import numpy as np
from matplotlib import pyplot as plt
from jaratoolbox import histologyanalysis as ha
reload(ha)
an = ha.AllenAnnotation()
imageDir5xMerge = '/home/nick/Desktop/mergedImages_anat036_5x_thal'
subject = 'anat036'
slices = ['p1d1', 'p1d2', 'p1d3']
ccfSlice = {'p1b6':163,
'p1c1':167,
'p1c2':171,
'p1c3':175,
'p1c4':179,
'p1c5':183,
'p1c6':187,
'p1d1':191,
'p1d2':195,
'p1d3':199,
'p1d4':203,
'p1d5':207,
'p1d6':211,
'p2a1':215,
'p2a2':219,
'p2a3':223,
'p2a4':226,
'p2a5':229,