from make_membrane_label import ImageFileProcessing __author__ = 'jhennies' imagePath = '/windows/mobi/h1.hci/isbi_2013/data/xytc_boundaries.bl1.ign4.sparse/' imageFile = 'xytc_boundaries.bl1.ign4.sparse1eq2.h5' imageName = None imageID = 0 # Initialize ImageFileProcessing object ifp = ImageFileProcessing() ifp.set_file(imagePath, imageFile, imageName, imageID) num_lab2 = ifp.count_labels(label=2) print num_lab2 num_lab1 = ifp.count_labels(label=1) print num_lab1 n_lab1 = num_lab1 - 100000 n_lab2 = num_lab2 - 100000 ifp.randomly_convert_labels_h5(from_label=1, to_label=0, n=n_lab1, file_name=None) ifp.randomly_convert_labels_h5( from_label=2, to_label=0, n=n_lab2, file_name='xytc_boundaries.bl1.ign4.sparse100k.h5') # ifp.randomly_convert_labels_h5(from_label=1, to_label=0, n=1000,
from make_membrane_label import ImageFileProcessing __author__ = 'jhennies' imagePath = '/windows/mobi/h1.hci/isbi_2013/prediction/20160105.blNone.ign4.ignl1.sparse10k/' imageFile = 'xytc_test-data-probs_probs.h5' imageName = None imageID = 0 # Initialize ImageFileProcessing object ifp = ImageFileProcessing() ifp.set_file(imagePath, imageFile, imageName, imageID) # Split data ifp.split_data_h5(file_name='split_data.h5', split_dimension=4, squeeze=True)
from make_membrane_label import ImageFileProcessing __author__ = 'jhennies' imagePath = '/windows/mobi/h1.hci/isbi_2013/data/' imageFile = 'xytc_boundaries.bl1.ign4.h5' imageName = None imageID = 0 # Initialize ImageFileProcessing object ifp = ImageFileProcessing() ifp.set_file(imagePath, imageFile, imageName, imageID) num_lab2 = ifp.count_labels(label=2) print num_lab2 num_lab1 = ifp.count_labels(label=1) print num_lab1 n = num_lab1 - num_lab2 if n > 0: ifp.randomly_convert_labels_h5(from_label=1, to_label=0, n=n, file_name='xytc_boundaries.bl1.ign4.sparse1eq2.h5') else: print 'n <= 0'
def make_h5_zeros(self, path, h5name, size): ifp = ImageFileProcessing() data = np.zeros(size, dtype=int) ifp.write_h5(path, data, h5name)
from make_membrane_label import ImageFileProcessing __author__ = 'jhennies' imagePath = '/windows/mobi/h1.hci/isbi_2013/data/' imageFile = 'test-input.h5' imageName = None imageID = 0 # Initialize ImageFileProcessing object ifp = ImageFileProcessing() ifp.set_file(imagePath, imageFile, imageName, imageID) # # Crop image if necessary, then re-run with cropped image # ifp.crop_h5((100, 100, 100)) # quit() ifp.stack_h5('test-data-probs.h5', '/windows/mobi/h1.hci/isbi_2013/data/test-probs-nn-m.h5', stack_id=0)