def _get_txt_acquisition(txt_acquisition, acquisition_name=None, verbose=False, filehandle=None): """ A generator the returns the acquisitions :param mcd_acquisition: :param acquisition: :param verbose: :return: """ if acquisition_name is None: acquisition_name='0' txt = txtparser.TxtParser(txt_acquisition, filehandle) if verbose: print('containing 1 acquisition') imc_img = txt.get_imc_acquisition() acquisition = acquisition_name yield (acquisition, imc_img)
get_ipython().magic('matplotlib notebook') # Define the variables: # The folder should contain the txt files from tunning tapes with 1 folder per day # In[214]: folder_name = '/mnt/bbvolume/hart_tma_data/20161025_tunning_tapes/' out_folder = '/home/vitoz/Data/Analysis/20161026_tuning_tape' # Load the txt files # In[12]: txt_parsers = [ txtparser.TxtParser(os.path.join(folder_name, subfol, fn)) for subfol in os.listdir(folder_name) for fn in os.listdir(os.path.join(folder_name, subfol)) ] # Following files were used: # In[13]: for p in txt_parsers: print(p.filename) # In[14]: imc_acs = [p.get_imc_acquisition() for p in txt_parsers]
metalDict[metal] = [bool(int(x)) for x in [fstack, istack]] fin.close() ## OUTPUT FILE LINKING ROI IDS TO ROI LABELS (IMAGE DESCRIPTION) roi_map = open(os.path.basename(args.INPUT_FILE) + '_ROI_map.csv', "w") ## USE DIFFERENT PARSERS CORRESPONDING TO THE INPUT FILE FORMAT file_type = re.sub(".*\.([^.]+)$", '\\1', args.INPUT_FILE.lower()) ## CONVERT INPUT_FILE TO TIFF AND WRITE RELEVANT TIFF IMAGES if file_type == "mcd": parser = mcdparser.McdParser(args.INPUT_FILE) acids = parser.acquisition_ids else: if file_type == "txt": parser = txtparser.TxtParser(args.INPUT_FILE) elif file_type == "tiff" or file_type == "tif": parser = omeparser.OmetiffParser(args.INPUT_FILE) else: print("{}: Invalid input file type - should be txt, tiff, or mcd!". format(file_type)) sys.exit(1) # THERE IS ONLY ONE ACQUISITION - ROI FOLDER NAMED ACCORDING TO INPUT FILENAME acids = [ re.sub('.txt|.tiff', '', os.path.basename(parser.filename).lower().replace(" ", "_")) ] for roi_number in acids: if file_type == "mcd":
def get_txt_aquisition(file_name): txt = txtparser.TxtParser(file_name) return txt.get_imc_acquisition()