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)