def build_dataset(self, datadir, spec, dset_name):
print(dset_name)
img = read_file(os.path.join(datadir, dset_name + "_img.h5"))
mit0 = read_file(os.path.join(datadir, dset_name + "_mit.h5")).astype("float32")
mit1 = read_file(os.path.join(datadir, dset_name + "_1eroded_mit.h5")).astype("float32")
mit2 = read_file(os.path.join(datadir, dset_name + "_2eroded_mit.h5")).astype("float32")
mit3 = read_file(os.path.join(datadir, dset_name + "_3eroded_mit.h5")).astype("float32")
# seg = read_file(os.path.join(datadir, dset_name + "_seg.h5"))
img = dp.transform.divideby(img, val=255.0, dtype="float32")
mit0[mit0 != 0] = 1 #Binarizing psds
mit1[mit1 != 0] = 1 #Binarizing psds
mit2[mit2 != 0] = 1 #Binarizing psds
mit3[mit3 != 0] = 1 #Binarizing psds
vd = dp.VolumeDataset()
vd.add_raw_data(key="input", data=img)
vd.add_raw_data(key="mit0_label", data=mit0)
vd.add_raw_data(key="mit1_label", data=mit1)
vd.add_raw_data(key="mit2_label", data=mit2)
vd.add_raw_data(key="mit3_label", data=mit3)
# vd.add_raw_data(key="psd_mask", data=msk)
vd.set_spec(spec)
return vd
def make_forward_scanner(data_name, opt):
# Read an EM image.
if opt.dummy:
img = np.random.rand(*opt.input_size[-3:]).astype('float32')
else:
img = emio.imread(os.path.join(opt.data_dir, data_name + '_img.h5'))
img = (img / 255.).astype('float32')
# Build Dataset.
vd = dp.VolumeDataset()
vd.add_raw_data(key='input', data=img)
vd.set_spec(opt.in_spec)
return dp.ForwardScanner(vd, opt.scan_spec, params=opt.scan_params)
def build_dataset(self):
# Image.
img = self.data['img']
# Segmentation.
seg = self.data['seg']
# Mask.
msk = self.data['msk_' + self.mode]
# Build dataset.
vd = dp.VolumeDataset()
vd.add_raw_data(key='input', data=img)
vd.add_raw_data(key='affinity', data=seg)
vd.add_raw_mask(key='affinity_mask', data=msk, loc=True)
vd.set_spec(self.spec)
return vd
def make_forward_scanner(dset_name, data_dir, input_spec,
scan_spec, scan_params, **params):
""" Creates a DataProvider ForwardScanner from a dset name """
# Reading EM image
# img = utils.read_h5(dset_name)
print("image path", os.path.join(data_dir, dset_name + "_img.h5"))
img = utils.read_h5(os.path.join(data_dir, dset_name + "_img.h5"))
img = (img / 255.).astype("float32")
# Creating DataProvider Dataset
vd = dp.VolumeDataset()
vd.add_raw_data(key="input", data=img)
vd.set_spec(input_spec)
# Returning DataProvider ForwardScanner
return dp.ForwardScanner(vd, scan_spec, params=scan_params)
def build_dataset(self, datadir, spec, dset_name):
print(dset_name)
img = read_file(os.path.join(datadir, dset_name + "_img.h5"))
psd = read_file(os.path.join(datadir,
dset_name + "_mit.h5")).astype("float32")
# seg = read_file(os.path.join(datadir, dset_name + "_seg.h5"))
img = dp.transform.divideby(img, val=255.0, dtype="float32")
psd[psd != 0] = 1 #Binarizing psds
# msk = (seg == 0).astype("float32") #Boundary mask
vd = dp.VolumeDataset()
vd.add_raw_data(key="input", data=img)
vd.add_raw_data(key="psd_label", data=psd)
# vd.add_raw_data(key="psd_mask", data=msk)
vd.set_spec(spec)
return vd
def build_dataset(self, datadir, spec, dset_name, erode):
print(dset_name)
img = read_file(os.path.join(datadir, dset_name + "_img.h5"))
mit_str = "_mit.h5"
if erode:
mit_str = "_"+str(erode)+"erode"+"_mit.h5"
mit = read_file(os.path.join(datadir, dset_name + mit_str)).astype("float32")
# print(img.shape)
# print(mit.shape)
# seg = read_file(os.path.join(datadir, dset_name + "_seg.h5"))
img = dp.transform.divideby(img, val=255.0, dtype="float32")
mit[mit != 0] = 1 #Binarizing psds
vd = dp.VolumeDataset()
vd.add_raw_data(key="input", data=img)
vd.add_raw_data(key="psd_label", data=mit)
# vd.add_raw_data(key="psd_mask", data=msk)
vd.set_spec(spec)
return vd
def build_dataset(self, datadir, spec, dset_name, resize):
print(dset_name)
img = read_file(os.path.join(datadir, dset_name + "_resized4_img.h5"))
psd = read_file(os.path.join(datadir, dset_name + "_resized4_blood.h5")).astype("float32")
# seg = read_file(os.path.join(datadir, dset_name + "_seg.h5"))
img = dp.transform.divideby(img, val=255.0, dtype="float32")
psd[psd != 0] = 1 #Binarizing psds
#if (resize != 1):
# img = utils.resize_image(img, resize)
# psd = scipy.misc.imresize(psd, 1.0/resize, interp="bilinear")
# msk = (seg == 0).astype("float32") #Boundary mask
vd = dp.VolumeDataset()
vd.add_raw_data(key="input", data=img)
vd.add_raw_data(key="psd_label", data=psd)
# vd.add_raw_data(key="psd_mask", data=msk)
vd.set_spec(spec)
return vd