In [1]:

    

%load_ext autoreload
%autoreload 2
import sys
import os
sys.path.append("/Users/palmer/Documents/python_codebase")
sys.path.append("/Users/palmer/Documents/python_codebase/pyimzml/")
import pyImagingMSpec.convert.h5_to_imzml as h5_to_imzml


    

In [ ]:

    

filein="/Users/palmer/Documents/tmp_data/spheroids/batch"
out_dr = '/Users/palmer/Documents/tmp_data/spheroids/imzml'
with open(filein,'r') as f:
    for line in f.readlines():
        fin = str(line).strip()
        if fin.startswith("#"):
            continue
        dr,ext = os.path.splitext(fin)
        fn = os.path.splitext(os.path.basename(fin)[0])
        fout = os.path.join(out_dr,fn+"imzML")
        print fin     , os.path.exists(fin)
        h5_to_imzml.centroidh5(fin,fout)


    

In [ ]:

    

files_in = [
    "/Volumes/alexandr/shared/imagingMS/External/Private/UoND/EricWeaver/Spheroids/14037s1_Spheroids24h_DHBSub/14037s1_Spheroids24h_DHBSub.h5",
    "/Volumes/alexandr/shared/imagingMS/External/Private/UoND/EricWeaver/Spheroids/14040s1_Spheroids12h_DHBSub/14040s1_Spheroids12h_DHBSub.h5",
    "/Volumes/alexandr/shared/imagingMS/External/Private/UoND/EricWeaver/Spheroids/Ctrl3s2_SpheroidsCtrl_DHBSub/Ctrl3s2_SpheroidsCtrl_DHBSub.h5",
    "/Volumes/alexandr/shared/imagingMS/External/Private/UoND/EricWeaver/Spheroids/Spheroids_sublimation_6h/Spheroids_sublimation_6h.h5"
]
out_dir = "/Users/palmer/Documents/tmp_data/old_spheroids/"

for file_in in files_in:
    assert os.path.isfile(file_in)
    fname = os.path.splitext(os.path.basename(file_in))[0]
    out_name = out_dir + fname + "_centroid.imzml"
    h5_to_imzml.centroidh5(file_in,out_name,smoothMethod='apodization')