def readWriteXMLTransform(projectPath,layerIndex,folder):
'''
1-Take the TrakEM project 'projectPath'
2-Read the transformation of the first patch of layer 'layerIndex'
3-Read the locations of the first patch of layer 'layerIndex' and layer '1-layerIndex'. This is used to calculate the offset of the EM and LM images in the initial transformation file
4-Write as a simple text file in folder + title of the project + InitialTransform.txt
'''
project = Project.openFSProject(projectPath, False)
layerset = project.getRootLayerSet()
layers = layerset.getLayers()
layer = layerset.getLayers().get(layerIndex)
patches = layer.getDisplayables(Patch)
t = patches.get(0).getAffineTransform()
transPath = folder + project.getTitle() + 'InitialTransform.txt.txt'
f = open(transPath,'w')
f.write( str(t.getScaleX()) + "\n")
f.write( str(t.getShearY())+ "\n")
f.write( str(t.getShearX())+ "\n")
f.write( str(t.getScaleY())+ "\n")
f.write( str(t.getTranslateX())+ "\n")
f.write( str(t.getTranslateY())+ "\n")
f.write ( str( layers.get(layerIndex).getDisplayables(Patch).get(0).getX() ) + '\n')
f.write ( str( layers.get(layerIndex).getDisplayables(Patch).get(0).getY() ) + '\n')
f.write ( str( layers.get(1-layerIndex).getDisplayables(Patch).get(0).getX() ) + '\n')
f.write ( str( layers.get(1-layerIndex).getDisplayables(Patch).get(0).getY() ) + '\n')
f.close()
IJ.log('Transformation saved in: ' + transPath)
# read the parameters of the transformations
trans = []
f = open(transPath,'r')
while 1:
line = f.readline()
if not line: break
IJ.log(line)
trans.append(float(line))
f.close
IJ.log('Transformation: ' + str(trans))
closeProject(project)
return trans
def openTrakemProject(path, mipmap = False): project = Project.openFSProject(cleanLinuxPath(path), False) return getProjectUtils(project, mipmap)
"/data/research/se/celegans/dataset3/N2DA_1430-2/M5/",
"/data/research/se/celegans/dataset3/N2DA_1430-2/N1/",
"/data/research/se/celegans/dataset3/N2DA_1430-2/N2/"
]
for i in range(len(proj_list)):
data_dir = proj_list[i]
proj_dir = os.path.join(data_dir, "montage_v1")
img_dir = os.path.join(data_dir, "transformed")
if not os.path.isdir(img_dir):
os.makedirs(img_dir)
proj_name = os.path.join(proj_dir, "montage_v1.xml")
project = Project.openFSProject(proj_name)
layerset = project.getRootLayerSet()
layer_list = layerset.getLayers()
fname_trans = os.path.join(data_dir, "transform.csv")
fw = open(fname_trans, "w")
for j in range(len(layer_list)):
layer = layer_list[j]
tiles = layer.getDisplayables(Patch)
patches = layer.getDisplayables(Patch)
for k in range(len(patches)):
