Save image after getTiles()

[beatrizserrano]

Hi!

I'd like to save the resulting image after getting a particular tile and plane. This is my code:

image = conn.getObject("Image", 567984)
cropParams = (336, 256, 672, 512) # x, y, width, height
zct_list = (0, 1, 0, cropParams) # z, channel, timepoint, size
imageROI = image.getPrimaryPixels().getTiles(zct_list)

Looks like imageROI is a generator object. I guess that this is the way of getting each tile for a give set of sizes. In my case, I just need one tile so I tried with imageROI.next() but it doesn't work. Also I've tried with imageROI.save(). Any thoughts on how to save this particular ROI?

[joshmoore]

You should be able to either wrap the generator with a list:

tile = list(getTiles())[0]

or iterate over it breaking as necessary:

for tile in getTiles():
   tile...
   break

What do you mean by "save"? Can you show us the rest of what you're trying to do? Perhaps similar is the getRohnTile method from https://github.com/IDR/idr-notebooks/blob/master/notebooks/RohnPhenotypeClustering.ipynb

[beatrizserrano]

Thanks, Josh. I was thinking to save the plane that the getRohnTile method returns into my tenancy but it doesn't make sense since I could compute the features directly over the numpy matrix. Here’s my code to do that:

from idr import connection
conn = connection()
image = conn.getObject("Image", 567984)

cropParams = (336, 256, 672, 512) # x, y, width, height
imageROI = image.getPrimaryPixels().getTile(theC=1, tile=cropParams)
conn.close()

from wndcharm.PyImageMatrix import PyImageMatrix
matrix = PyImageMatrix()
matrix.allocate(imageROI.shape[1], imageROI.shape[0])
numpy_matrix = matrix.as_ndarray()
numpy_matrix[:] = imageROI
from wndcharm.FeatureVector import FeatureVector
fv = FeatureVector(name='FromNumpyMatrix', long=True, original_px_plane=matrix)
fv.GenerateFeatures(quiet=False, write_to_disk=True)

However, I'm now facing a new issue :) Wnd-charm doesn't seem to be installed, I've tried this but to no avail:

!conda install --yes --prefix {sys.prefix} wndcharm

Is there any way to use wndcharm package in my notebook?

Thanks!

[joshmoore]

I was thinking to save the plane that the getRohnTile method returns into my tenancy but it doesn't make sense since I could compute the features directly over the numpy matrix.

Exactly. For this preliminary testing, the binary day stays in the IDR jupyter and some (minimal) processing can be done on it. When the full version using the public API, the communication overhead would be in getting thetile to your tenancy, where you then do the processing.

Is there any way to use wndcharm package in my notebook?

I haven't tested this thoroughly, but this looks like it would get you started:

%%bash
conda install -y -c eumetsat fftw3
conda install -y -c anaconda libtiff
test -e wnd-charm || git clone --depth=1 https://github.com/wnd-charm/wnd-charm.git wnd-charm

cd wnd-charm

%%bash
touch aclocal.m4 Makefile.in configure config.h.in
export CFLAGS="-L/opt/conda/lib -I/opt/conda/include"
export CXXFLAGS="$CFLAGS"
./configure --prefix=/opt/conda/
make install

afterwards

!/opt/conda/bin/wndchrm

produces

wndchrm 1.60-de98947.  Laboratory of Genetics/NIA/NIH 
usage: 
======
wndchrm [ train | test | classify | check ] [-mtslcdowfrijnpqvNSBACDTh] [<dataset>|<train set>] [<test set>|<feature file>] [<report_file>]