Commits

Olivier Debeir committed 5b77bdd

add test hdf5 file

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Files changed (5)

 import context
 from test import test_N
 
-test_N()
+test_N(n_list=[8])
 * :download:`some marks for the last sequence frame (.CSV) <../test/data/rev_marks.csv>`
 
 * :download:`small zipped phase contrast sequence (30 frames) (.ZIP) <../test/data/seq0_extract.zip>`
+
+* :download:`HDF5 test file (31 cells/30 frames) (.HDF5) <../test/data/test_rev.hdf5>`
 to the shape of the inner triangles which are put in a reversed direction. This option gives better results for the soma
 detection.
 
+The following figure illustrate how the space around a cell is decomposed into pies (N=8). Large pies are in charge of
+finding the halo, smaller inner pies are responsible for the soma.
+
+.. plot:: code/ex2.py
+
+
+
 Implementation
 ------------------
 

ivctrack/cellmodel.py

     experiment = Experiment(reader,exp_name='Test')
 
     #mark initial cell position (may be in the middle of the sequence
-    marks = import_marks('../test/data/fwd_marks.csv')
+    marks = import_marks('../test/data/rev_marks.csv')
     params = {'N':8,'radius_halo':20,'radius_soma':12,'exp_halo':10,'exp_soma':2,'niter':10,'alpha':.75}
 
     track_list = []
     experiment.do_tracking('fwd')
 
     #save data to file
-    experiment.save_hdf5('../test/temp/test.hdf5')
+    experiment.save_hdf5('../test/temp/test_rev.hdf5')
 
 if __name__ == "__main__":
 

test/test_model.py

 
     plt.show()
 
-def test_N():
+def test_N(n_list=[3,5,8,16,32]):
     """Test function: illustrate the N parameter (#of pies of the model)
     """
     im = imread(os.path.join(os.path.dirname(__file__),'../test/data/exp0001.jpg'))
     cellLocations = [(340,190),(474,331),(120,231)]
-    for N in [3,5,8,16,32]:
+    for N in n_list:
         fig = plt.figure()
         ax = fig.add_subplot(111)
         ax.imshow(im, interpolation='nearest')