open images in a Python's script

[MLB]

Hi,

We have developp a script with numpy and nibabel library.
In script editor with Jython execnet for Icy, we would like to open the results (images).
How can we do this ?
 
gateway.get ?
Do you have any examples ?

Thank you
Marie Laure

[Osvaldo Fuica]

Hi There, 

You can find basic documentation and examples on this url http://icy.bioimageanalysis.org/plugin/Jython_execnet_for_Icy

Best, 

Osvaldo

[MLB]

Thank you for your answer Osvaldo,

We have developped a script in python, and we would like at the end to open the results.

This is a sum up of our script :

from icy.main import Icy
from icy.sequence import Sequence
from icyexecnetgateway import IcyExecnetGateway


code = """
import sys
sys.path.append('/Users/sylvain/Desktop')
import Algo_Recalage
from Algo_Recalage import Algo
Algo(0,30,/Users/sylvain/Desktop/img.nii)
"""

--------> Icy.open("/Users/sylvain/Desktop/img-Res.nii") ' this is my hard issue :-)


with IcyExecnetGateway(python_path = "/Users/Shared/Sofwares/anaconda/bin/python") as gateway:
 gateway.remote_exec(code)

Thank you for your help,

Marie Laure

[Osvaldo Fuica]

Ok, 

I understand your problem.

The Icy open should happen outside of the "code" (That is remote code)

So, you will need send your information from remote to the local.

There you have an example that could be util for you.

At the moment a limitation that i am seeing is that gateway send and receive only support 2D data...

from icy.main import Icy

from icy.sequence import Sequence

from icy.image import IcyBufferedImageUtil

from icyexecnetgateway import IcyExecnetGateway, unpack_image

code = """

from numpyexecnet import pack_image

from nibabel.testing import data_path

import os

import numpy as np

import nibabel as nib

example_filename = os.path.join(data_path, 'example4d.nii.gz')

img = nib.load(example_filename)

data = img.get_data()

shape = data.shape

xSize = data.shape[0]

ySize = data.shape[1]

zSize = data.shape[2]

tSize = data.shape[3]

for z in range(0, zSize):

zdata = data[:, :, z, 0]

packed_image = pack_image(zdata)

channel.send(packed_image)

"""

with IcyExecnetGateway() as gateway:

gateway.remote_exec(code)

sequence = None

while True:

try:

packed_image = gateway.receive()

unpacked_image = unpack_image(packed_image)

if sequence == None:

sequence = Sequence(unpacked_image)

continue

sequence.addImage(unpacked_image)

except EOFError as e:

Icy.addSequence(sequence)

break

[Osvaldo Fuica]

You can also open the file that you want directly. In this case Icy supports .nii format file.

Here a small example.

from icy.file import Loader

image = "/Users/osvaldo/Desktop/example4d.nii"

Loader.load(image, False)

Best.

[MLB]

Hi Osvaldo,
Thank you very much, it runs well !

:-))))

We had an other issue with icy on windows.
On mac, it ran well with this whole path  : /Users/Shared/Sofwares/anaconda/bin/python

with IcyExecnetGateway(python_path = "/Users/Shared/Sofwares/anaconda/bin/python") as gateway:
 gateway.remote_exec(code)


On windows we just need to put  python.exe instead of C:\Anaconda2\python.exe



with IcyExecnetGateway(python_path="python.exe") as gateway:
    gateway.remote_exec(code)

In case that somebody has the same issue.

Marie Laure & Sylvain

[MLB]

Hi,
Is it possible to add some variables to the external script ?

For example give the variable Reframe from an input of the window pythonscript to the external script ?

Thank you for your help and have a nice summer !

Marie Laure

Saisissez le code ici...from icy.main import Icy

from icy.sequence import Sequence
from icyexecnetgateway import IcyExecnetGateway

from icy.image import IcyBufferedImageUtil

RefFrame = input0


code = """
import sys
sys.path.append('C://MarieLaure/homestrain/script')
import scriptpyhton
from scriptpyhtonimport functionpython
InputSequence="C://MarieLaure/homestrain/tmp/tmpfile.nii"
pathsave="C://MarieLaure/homestrain/data/Res22aout/"
FirstFrame=1
LastFrame=5
StepFrames=1
TimeIsZaxis=0
Prefix_Outputs='out'
maskRefFrame='NULL'
functionpython(InputSequence,pathsave,FirstFrame,LastFrame,StepFrames,RefFrame,TimeIsZaxis,Prefix_Outputs,maskRefFrame)

[Osvaldo Fuica]

Hi, 

I think is only possible add variables using Protocols, you can do that just copy and paste your code in python script box, and creating the correspondent boxes or inputs. 

Anyway, I let you this example that can be usefully for you and others :)

Have a nice summer too!.

Kind Regards, 

Osvaldo