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()