In [1]:

    

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


    

In [2]:

    

fin = "/Users/palmer/Documents/tmp_data/RatBrain_IMS/single_smooth/Rat_brain_1M_50um_97_trim_centoids_IMS.hdf5"
fout = "/Users/palmer/Documents/tmp_data/RatBrain_IMS/single_smooth/Rat_brain_1M_50um_97_trim_centoids_IMS.imzML"
h5_to_imzml.hdf5_centroids_IMS(fin,fout)


    

    




file loaded
dim: 223 x 257
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finished!






    




/usr/local/lib/python2.7/site-packages/numpy/core/_methods.py:59: RuntimeWarning: Mean of empty slice.
  warnings.warn("Mean of empty slice.", RuntimeWarning)
/usr/local/lib/python2.7/site-packages/numpy/core/_methods.py:70: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)

In [3]:

    

from pyImagingMSpec.hdf5.inMemoryIMS import inMemoryIMS
fout = "/Users/palmer/Documents/tmp_data/UCSD01902/UCSD_01902_centroids_IMS.imzML"

imsDataset = inMemoryIMS(fout,cache_spectra=True,min_mz=100., max_mz=200.)


    

    




TODO: convert indices into real world coordinates
loaded spectra
file loaded

In [4]:

    

import matplotlib.pyplot as plt
import numpy as np
%matplotlib notebook
ionIm = imsDataset.get_ion_image(np.asarray([174.492797852,]),np.asarray([100,]))
im = ionIm.xic_to_image(0)
plt.figure()
plt.imshow(im)
plt.clim([np.min(ionIm.xic),np.percentile(ionIm.xic,99)])
plt.colorbar()
plt.show()


    

    




/usr/local/lib/python2.7/site-packages/IPython/kernel/__init__.py:13: ShimWarning: The `IPython.kernel` package has been deprecated. You should import from ipykernel or jupyter_client instead.
  "You should import from ipykernel or jupyter_client instead.", ShimWarning)






    















    

In [5]:

    

print imsDataset.mz_list[np.argmax(imsDataset.count_list)]


    

    




174.492797852

In [6]:

    

filename = "/Volumes/alexandr/palmer/data_store/IMS/2015_08/20150813_ADP_KS_DHBsub_PRM_70x55_15um_fullms/20150813_ADP_KS_DHBsub_mouseBrain_70x55_15um_fullms.imzML"
imsDataset2 = inMemoryIMS(filename,cache_spectra=True)


    

    




TODO: convert indices into real world coordinates
loaded spectra
file loaded

In [7]:

    

ionIm = imsDataset2.get_ion_image(np.asarray([730.5745,]),np.asarray([100,]))
im = ionIm.xic_to_image(0)
plt.figure()
plt.imshow(im,interpolation='nearest')
plt.clim([np.min(ionIm.xic),np.percentile(ionIm.xic,99)])
plt.colorbar()
plt.show()