In [1]:

    

%pylab inline
from glob import glob
from leicaexperiment import Experiment as LeicaExperiment
from tifffile import imread, imsave, imshow

experiments = glob('/Users/arve/Dokumenter/TFY4500/unstained/experiment--*')

leica_experiments = []
for e in experiments:
    leica_experiments.append(LeicaExperiment(e))


    

    




Populating the interactive namespace from numpy and matplotlib

In [2]:

    

#for experiment in leica_experiments:
experiment = leica_experiments[0]
well = experiment.wells[0] # only have one
img = well.merge()
imshow(img, figure=figure(figsize=(12,12)))


    

    




merge(..) is depreciated, use stitch() instead.






    
Out[2]:





(<matplotlib.figure.Figure at 0x112c330b8>,
 <matplotlib.axes._subplots.AxesSubplot at 0x1131ab4e0>,
 <matplotlib.image.AxesImage at 0x113273ef0>)






    

In [3]:

    

img.shape


    

    
Out[3]:





(1024, 1024)

In [4]:

    

type(img[0,0])


    

    
Out[4]:





numpy.float64

In [2]:

    

experiment = leica_experiments[1]
experiment.wells[0].z_stacks


    

    
Out[2]:





10

In [3]:

    

img = experiment.wells[0].merge(0)
img2 = experiment.wells[0].merge(5)


    

    




/Users/arve/Dokumenter/TFY4500/comparison/experiment--2014_11_12_13_14_42/slide--S00/chamber--U00--V00/field--X00--Y00/image--L00--S00--U00--V00--J08--E00--O00--X00--Y00--T00--Z00--C00.ome.tif
/Users/arve/Dokumenter/TFY4500/comparison/experiment--2014_11_12_13_14_42/slide--S00/chamber--U00--V00/field--X00--Y00/image--L00--S00--U00--V00--J08--E00--O00--X00--Y00--T00--Z00--C01.ome.tif
/Users/arve/Dokumenter/TFY4500/comparison/experiment--2014_11_12_13_14_42/slide--S00/chamber--U00--V00/field--X00--Y01/image--L00--S00--U00--V00--J08--E00--O00--X00--Y01--T00--Z00--C00.ome.tif
/Users/arve/Dokumenter/TFY4500/comparison/experiment--2014_11_12_13_14_42/slide--S00/chamber--U00--V00/field--X00--Y01/image--L00--S00--U00--V00--J08--E00--O00--X00--Y01--T00--Z00--C01.ome.tif
/Users/arve/Dokumenter/TFY4500/comparison/experiment--2014_11_12_13_14_42/slide--S00/chamber--U00--V00/field--X01--Y00/image--L00--S00--U00--V00--J08--E00--O00--X01--Y00--T00--Z00--C00.ome.tif
/Users/arve/Dokumenter/TFY4500/comparison/experiment--2014_11_12_13_14_42/slide--S00/chamber--U00--V00/field--X01--Y00/image--L00--S00--U00--V00--J08--E00--O00--X01--Y00--T00--Z00--C01.ome.tif
/Users/arve/Dokumenter/TFY4500/comparison/experiment--2014_11_12_13_14_42/slide--S00/chamber--U00--V00/field--X01--Y01/image--L00--S00--U00--V00--J08--E00--O00--X01--Y01--T00--Z00--C00.ome.tif
/Users/arve/Dokumenter/TFY4500/comparison/experiment--2014_11_12_13_14_42/slide--S00/chamber--U00--V00/field--X01--Y01/image--L00--S00--U00--V00--J08--E00--O00--X01--Y01--T00--Z00--C01.ome.tif
/Users/arve/Dokumenter/TFY4500/comparison/experiment--2014_11_12_13_14_42/slide--S00/chamber--U00--V00/field--X00--Y00/image--L00--S00--U00--V00--J08--E00--O00--X00--Y00--T00--Z05--C00.ome.tif
/Users/arve/Dokumenter/TFY4500/comparison/experiment--2014_11_12_13_14_42/slide--S00/chamber--U00--V00/field--X00--Y00/image--L00--S00--U00--V00--J08--E00--O00--X00--Y00--T00--Z05--C01.ome.tif
/Users/arve/Dokumenter/TFY4500/comparison/experiment--2014_11_12_13_14_42/slide--S00/chamber--U00--V00/field--X00--Y01/image--L00--S00--U00--V00--J08--E00--O00--X00--Y01--T00--Z05--C00.ome.tif
/Users/arve/Dokumenter/TFY4500/comparison/experiment--2014_11_12_13_14_42/slide--S00/chamber--U00--V00/field--X00--Y01/image--L00--S00--U00--V00--J08--E00--O00--X00--Y01--T00--Z05--C01.ome.tif
/Users/arve/Dokumenter/TFY4500/comparison/experiment--2014_11_12_13_14_42/slide--S00/chamber--U00--V00/field--X01--Y00/image--L00--S00--U00--V00--J08--E00--O00--X01--Y00--T00--Z05--C00.ome.tif
/Users/arve/Dokumenter/TFY4500/comparison/experiment--2014_11_12_13_14_42/slide--S00/chamber--U00--V00/field--X01--Y00/image--L00--S00--U00--V00--J08--E00--O00--X01--Y00--T00--Z05--C01.ome.tif
/Users/arve/Dokumenter/TFY4500/comparison/experiment--2014_11_12_13_14_42/slide--S00/chamber--U00--V00/field--X01--Y01/image--L00--S00--U00--V00--J08--E00--O00--X01--Y01--T00--Z05--C00.ome.tif
/Users/arve/Dokumenter/TFY4500/comparison/experiment--2014_11_12_13_14_42/slide--S00/chamber--U00--V00/field--X01--Y01/image--L00--S00--U00--V00--J08--E00--O00--X01--Y01--T00--Z05--C01.ome.tif






    




/Users/arve/.virtualenvs/3.4/lib/python3.4/site-packages/tifffile.py:1030: UserWarning: ome-xml: invalid TiffData index
  warnings.warn("ome-xml: invalid TiffData index")

In [19]:

    

f = experiment.wells[0].fields[0].images[9].fullpath


    

In [21]:

    

img = imread(f)
f


    

    
Out[21]:





'/Users/arve/Dokumenter/TFY4500/comparison/experiment--2014_11_12_13_14_42/slide--S00/chamber--U00--V00/field--X00--Y00/image--L00--S00--U00--V00--J08--E00--O00--X00--Y00--T00--Z04--C01.ome.tif'

In [23]:

    

%run ../../common.ipynb
gimshow(img)
img.shape


    

    




Populating the interactive namespace from numpy and matplotlib






    




WARNING: pylab import has clobbered these variables: ['imsave', 'imread']
`%matplotlib` prevents importing * from pylab and numpy






    
Out[23]:





(512, 512)






    

In [14]:

    

imshow(img)
imshow(img2)


    

    
Out[14]:





(<matplotlib.figure.Figure at 0x107991ef0>,
 <matplotlib.axes._subplots.AxesSubplot at 0x106c35940>,
 <matplotlib.image.AxesImage at 0x107a2e278>)