def test_func():
"""You can conver a single smv file to 3D tiff by specifying
data_path, output_path, fileName and set the SigleConvert flag to 1.
You can conver a batch of smv files to 3D tiffs by specifying
root data_path, output_path and set the BatchConvert flag to 1.
"""
## Please specify paths ##
data_path = '/home/yanbin/Tomosynthesis/data/SAP_test_datasets/Screening_30_cases/6002/'
output_path = '/home/yanbin/Tomosynthesis/script_test/'
fileName = '6002L06.smv'
## Please specify Parameters ##
BatchConvert = 0
SigleConvert = 0
dim = 3
## data_path check
if not os.path.isdir(data_path):
print "Data directory:\n"+ data_path +"\ndoes not exist"
sys.exit()
## Format convert batch
if BatchConvert == 1:
print 'here'
dir_list = os.listdir(data_path)
print dir_list
for dirc in dir_list:
print dirc
if os.path.isdir(data_path + dirc):
# make directory for output files
opath = output_path + dirc + '/'
print opath
if not os.path.isdir(opath):
os.makedirs(opath)
file_list = os.listdir(data_path + dirc)
for fil in file_list:
im = ImageIO.imReader(data_path + dirc + '/', fil, 'smv')
ImageIO.imWriter(opath, fil.strip('smv') + 'tif',im,dim)
## Format convert single
if SigleConvert == 1:
im = ImageIO.imReader(data_path,fileName, 'smv')
ImageIO.imWriter(output_path, fileName.strip('smv') + 'tif',im, dim)
def main():
## Please specify paths ##
data_path = '/home/yanbin/Tomosynthesis/data/SAP_test_datasets/Screening_30_cases/'
output_path = '/home/yanbin/Tomosynthesis/data/tiffs_3d/'
exe_path= '/home/yanbin/Tomosynthesis/code/'
## Please specify Run Flags ##
FormatConvert = 1
AWDenoising = 0
ContrastEnhancement = 0
## Please specify parameters ##
dim = 3 # For format convert: save as 2d slices / 3d stack
opt = 'asymptotic' # For AWdenoising inverse transform options
block_m=5
block_n=5 # For AWdenoising Wiener filter window size block_m = block_n
###################### Avalability Check #######################
# data_path check
if not os.path.isdir(data_path):
print "Data directory:\n"+ data_path +"\ndoes not exist"
sys.exit()
# exe_path check
if not os.path.isdir(exe_path):
print "Executable directory:\n"+ exe_path +"\ndoes not exist"
sys.exit()
###################### Format Convert #######################
if FormatConvert == 1:
dir_list = os.listdir(data_path)
print dir_list
for dirc in dir_list:
print dirc
if os.path.isdir(data_path + dirc):
# make directory for output files
opath = output_path + dirc + '/'
print opath
if not os.path.isdir(opath):
os.makedirs(opath)
file_list = os.listdir(data_path + dirc)
for fil in file_list:
im = ImageIO.imReader(data_path + dirc + '/', fil, 'smv')
ImageIO.imWriter(opath, fil.strip('smv') + 'tif',im,dim)
############################# Denoising ##########################
if AWDenoising == 1:
dir_list = os.listdir(data_path)
print dir_list
for dirc in dir_list:
print dirc
if os.path.isdir(data_path + dirc):
# make directory for output files
opath = output_path + dirc + '/'
print opath
if not os.path.isdir(opath):
os.makedirs(opath)
file_list = os.listdir(data_path + dirc)
for fil in file_list:
im = ImageIO.imReader(data_path + dirc + '/', fil, 'tif',2)
denoised = AT_denoising.DenoisingAW(im.data[0], opt = 'asymptotic', block_m=5,block_n=5)
tiffLib.imsave(opath + 'denoised_' + fil,denoised)
###################### Contrast enhancement #######################
if ContrastEnhancement == 1:
dir_list = os.listdir(data_path)
print dir_list
for dirc in dir_list:
print dirc
if os.path.isdir(data_path + dirc):
# make directory for output files
opath = output_path + dirc + '/'
print opath
if not os.path.isdir(opath):
os.makedirs(opath)
file_list = os.listdir(data_path + dirc)
for fil in file_list:
im = ImageIO.imReader(data_path + dirc + '/', fil, 'tif',2)
enhanced = histEqualization.histEqualization(im.data[0], 16)
tiffLib.imsave(opath + 'enhanced_' + fil,enhanced)
