def test_graph_from_image(visual=False):
im = imread("segmentation.inr.gz")
graph = graph_from_image(im)
if visual:
Viewer.display(
graph2pglscene(graph, graph.vertex_property('barycenter'),
graph.vertex_property('L1')))
def read_image_path(urls, mimetype_in, mimetype_out):
if isinstance(urls, basestring):
urls = [urls]
for url in urls:
url = path(url)
if url.exists():
try:
data = imread(url)
except Exception, e:
e = MimeConversionError(url, mimetype_in, mimetype_out, e)
raise e
else:
return data, {}
def compute_cell_separation(mat):
"""
Function creating a space between cells for display.
Change the shared voxel between two cell to 0 so you can clearly see the seperations bewteen cells.
"""
import scipy.nd as nd
import numpy as np
import copy
sep=nd.laplace(mat)
sep2=copy.copy(sep)
sep2[np.where(mat==1)]=0
sep2[np.where(sep==0)]=1
sep2[np.where(sep!=0)]=0
mat=mat*sep2
del sep2,sep
return mat
if __name__ == '__main__':
im1 = imread('../../../test/segmentation.inr.gz')
im1a=SpatialImageAnalysis(im1)
dictionary=dict(zip(im1a.labels(), im1a.volume()))
labs=im1a.labels()
L1=im1a.L1()[1]
filtre=[i for i in labs if i not in L1]
display3D(im1,filtre, dictionary, rainbow_full)
self._im_view.rotate(-1)
self.update_pix()
def rotate_right(self):
res = self._label._resolution
self._label._resolution = res[1], res[0]
self._im_view.rotate(1)
self.update_pix()
if __name__ == '__main__':
from openalea.deploy.shared_data import shared_data
from openalea.image.serial.basics import imread
import openalea.oalab
img_path = shared_data(openalea.oalab, 'icons/Crystal_Clear_app_clock.png')
img = imread(img_path)
import numpy
matrix = numpy.zeros((100, 100, 100), dtype=numpy.uint8)
matrix[90:100, :10, :10] = 1
matrix[:10, 90:100, :10] = 2
matrix[:10, :10, 90:100] = 3
img3d = SpatialImage(matrix)
instance = QtGui.QApplication.instance()
if instance is None:
app = QtGui.QApplication([])
else:
app = instance
slider = ImageStackViewerWidget()
def test_graph_from_image(visual = False):
im = imread("segmentation.inr.gz")
graph = graph_from_image(im)
if visual :
Viewer.display(graph2pglscene(graph,graph.vertex_property('barycenter'),graph.vertex_property('L1')))
w.write()
def compute_cell_separation(mat):
"""
Function creating a space between cells for display.
Change the shared voxel between two cell to 0 so you can clearly see the seperations bewteen cells.
"""
import scipy.nd as nd
import numpy as np
import copy
sep = nd.laplace(mat)
sep2 = copy.copy(sep)
sep2[np.where(mat == 1)] = 0
sep2[np.where(sep == 0)] = 1
sep2[np.where(sep != 0)] = 0
mat = mat * sep2
del sep2, sep
return mat
if __name__ == '__main__':
im1 = imread('../../../test/segmentation.inr.gz')
im1a = SpatialImageAnalysis(im1)
dictionary = dict(zip(im1a.labels(), im1a.volume()))
labs = im1a.labels()
L1 = im1a.L1()[1]
filtre = [i for i in labs if i not in L1]
display3D(im1, filtre, dictionary, rainbow_full)
def wra_imread (filename) :
return imread(filename)
