def _get_mcd_acquisition(mcd_acquisition,
acquisition='all',
verbose=False,
filehandle=None):
"""
A generator the returns the acquisitions
:param mcd_acquisition:
:abstractparseram acquisition:
:param verbose:
:return:
"""
with mcdparser.McdParser(mcd_acquisition, filehandle) as mcd:
n_ac = mcd.n_acquisitions
if verbose:
print('containing %i acquisitions:' % n_ac)
ac_ids = mcd.acquisition_ids
if verbose:
for aid in ac_ids:
print('%s \n' % aid)
print('Print acquisition: %s' % acquisition)
if acquisition == 'all':
acquisitions = ac_ids
else:
acquisitions = [acquisition]
for aid in acquisitions:
imc_img = mcd.get_imc_acquisition(aid)
acquisition = aid
yield (acquisition, imc_img)
def load(cls, slide: Slide) -> Slide:
slide_path = slide.slide_path
with mcdparser.McdParser(slide_path) as mcd:
slide_item = mcd.meta.objects['Slide']['0']
file_name = os.path.basename(slide_path)
slide.meta = slide_item.properties
for panorama_item in slide_item.childs['Panorama'].values():
panorama = Panorama(panorama_item.properties['Description'], panorama_item.properties)
slide.addChild(panorama)
if 'AcquisitionROI' in panorama_item.childs:
for acquisition_roi_item in panorama_item.childs['AcquisitionROI'].values():
roi_points: List[ROIPoint] = list()
for roi_point_item in acquisition_roi_item.childs['ROIPoint'].values():
roi_point = ROIPoint(roi_point_item.metaname, roi_point_item.properties)
roi_points.append(roi_point)
acquisition_roi = AcquisitionROI(acquisition_roi_item.metaname, acquisition_roi_item.properties, roi_points)
panorama.add_acquisition_roi(acquisition_roi)
for acquisition_item in acquisition_roi_item.childs['Acquisition'].values():
# Dict key should be str!
acquisition = Acquisition(acquisition_item.properties['Description'], acquisition_item.properties)
acquisition_roi.add_acquisition(acquisition)
imc_acquisition = mcd.get_imc_acquisition(acquisition.id)
for i in range(imc_acquisition.n_channels):
meta = dict()
label = imc_acquisition.channel_labels[i]
meta['Label'] = label
meta['Metal'] = imc_acquisition.channel_metals[i]
meta['Mass'] = imc_acquisition.channel_mass[i]
img = imc_acquisition.get_img_by_label(label)
channel = Channel(label, meta, img)
acquisition.add_channel(channel)
return slide
def save_mcd_tiff(mcd_filename, acquisition='all', tifftype='ome', compression=0, outname=None, outpath=0,verbose=False):
"""
:param mcd_filename:
:param acquisition:
:param tifftype:
:param compression:
:param outname:
:param outpath:
:return:
"""
# parse the arguments
args = parser.parse_args()
if verbose:
print('Load filename %s' %mcd_filename)
if outname is None:
outname = os.path.split(mcd_filename)[1]
outname = outname.replace('.mcd', '')
if outpath is None:
outpath = os.path.split(mcd_filename)[0]
with mcdparser.McdParser(mcd_filename) as mcd:
n_ac = mcd.n_acquisitions
if verbose:
print('containing %i acquisitions:' % n_ac)
ac_ids = mcd.acquisition_ids
if verbose:
for aid in ac_ids:
print('%s \n' %aid)
print('Print acquisition: %s' %acquisition)
if args.acquisition == 'all':
acquisitions = ac_ids
else:
acquisitions = [acquisition]
for aid in acquisitions:
imc_img = mcd.get_imc_acquisition(aid)
cur_outname = outname + '_a' + aid
if tifftype == 'ome':
cur_outname += '.ome.tiff'
else:
cur_outname +='.tiff'
cur_outname = os.path.join(outpath, cur_outname)
if verbose:
print('Save %s as %s' %(aid,cur_outname))
iw = imc_img.get_image_writer(cur_outname)
iw.save_image(mode=tifftype, compression=compression)
if verbose:
print('Finished!')
def get_mcd_aquisition(file_name, roi_name):
""" Extracts the acquisition specified by the ROI name from a mcd file"""
mcd = mcdparser.McdParser(file_name)
roi_ids = {mcd.get_acquisition_description(id) : id for id in mcd.acquisition_ids}
if roi_name not in roi_ids.keys():
print(f"ROI not present: {roi_name}")
print("Available ROIs: " + "\n".join(roi_ids.keys()))
sys.exit(1)
return mcd.get_imc_acquisition(roi_ids[roi_name])
## CREATE DICTIONARY
metal = metal.upper()
if metal not in metalDict:
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(" ", "_"))
if fstack not in ['0', '1'] or istack not in ['0', '1']:
print("{}: Invalid column code - should be 0 or 1!\nLine: '{}'".format(
ERROR_STR, line.strip()))
sys.exit(1)
## CREATE DICTIONARY
metal = metal.upper()
if metal not in metalDict:
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.MCD_FILE) + '_ROI_map.csv', "w")
## COMVERT MCD TO TIFF AND WRITE RELEVANT TIFF IMAGES
mcd = mcdparser.McdParser(args.MCD_FILE)
for acid in mcd.acquisition_ids:
imc_ac = mcd.get_imc_acquisition(acid)
roi_label = mcd.get_acquisition_description(acid)
roi_map.write("roi_%s,%s" % (acid, roi_label) + "\n")
for l, m in zip(imc_ac.channel_labels, imc_ac.channel_metals):
filename = "%s.tiff" % (l)
## WRITE TO APPROPRIATE DIRECTORY
metal = l.split('_')[0].upper()
if metal in metalDict:
for i, j in enumerate(HEADER[1:]):
if metalDict[metal][i]:
dirname = "roi_%s/%s" % (acid, j)
if not os.path.exists(dirname):
os.makedirs(dirname)
if remove_folder:
os.removedirs(out_folder)
def _write_acquisition(self, ac, out_folder):
file_end = '_ac.ome.tiff'
if ac.image_description is None:
ac_id = ac.image_ID
fn = self.meta.get_object(mcdmeta.ACQUISITION, ac_id).metaname
else:
fn = ac.image_description
img_writer = ac.get_image_writer(
os.path.join(out_folder, fn + file_end))
img_writer.save_image(mode='ome')
def _find_ac_metaname_from_txt_fn(self, ac):
raise NotImplementedError
if __name__ == '__main__':
import imctools.io.mcdparser as mcdp
#fn_mcd = '/home/vitoz/temp/txtvsmcd/20170805_p60-63_slide6_ac1_vz.mcd'
#fn_mcd = '/mnt/imls-bod/VitoZ/Spheres/20161130_p25_slide2_ac1/20161130_p25_slide2_ac1.mcd'
#fn_mcd='/mnt/imls-bod/VitoZ/Spheres/20161005_IS2362_4_site1_ac1/20161005_IS2362_4_site1_ac1.mcd'
# an example of not functional mcd but working txt
# fn_mcd = /mnt/imls-bod/DanielS/ACD/IMC\ 2.06/Her2_grade3
fn_mcd = '/mnt/imls-bod/VitoZ/Spheres/20161018_OCT1_slide4_ac1/20161018_OCT1_slide4_ac1.mcd'
mcd = mcdp.McdParser(fn_mcd)
mcd.save_meta_xml('/home/vitoz/temp/')
ifw = ImcFolderWriter('/home/vitoz/temp/', mcddata=mcd)
ifw.write_imc_folder()