/
create_views.py
executable file
·86 lines (66 loc) · 2.79 KB
/
create_views.py
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#!/usr/bin/env python
import argparse
import os
import json
#import renderapi
import random
import requests
import tifffile
from PIL import Image
from io import BytesIO
import numpy
def convert(value, numofdigits):
strval = str(value)
lenstr = len(strval)
if lenstr > numofdigits:
print ("Cannot create a string smaller than needed")
exit(0)
else:
prefix = "0"*(numofdigits - lenstr)
strval = prefix+strval
#print strval
return strval
if __name__ == '__main__':
parser = argparse.ArgumentParser(description = "Create Views for Movie")
parser.add_argument('--inputStack',nargs='+',help='Name of input stack',type=str)
parser.add_argument('--outputDirectory',nargs=1,help='Output directory',type=str)
parser.add_argument('--scale',nargs=1,help='Scale of image',type=str)
parser.add_argument('--firstz',nargs=1,help='First z value ',type=int)
parser.add_argument('--lastz',nargs=1,help='Last z value ',type=int)
parser.add_argument('--skip',nargs=1,help='Number of Sections to skip over ',type=int)
args = parser.parse_args()
inputStack = args.inputStack[0]
outputDirectory = args.outputDirectory[0]
scale = args.scale[0]
firstz = args.firstz[0]
lastz = args.lastz[0]
print inputStack
print scale
if not os.path.isdir(outputDirectory):
os.makedirs(outputDirectory)
z = firstz
print z
while z <= lastz:
a = z
#request_url = "http://ibs-forrestc-ux1.corp.alleninstitute.org:8082/render-ws/v1/owner/Sharmishtaas/project/M270907_Scnn1aTg2Tdt_13/stack/%s/z/%s/jpeg-image?scale=%s"%(inputStack,str(z),scale)
request_url = "http://ibs-forrestc-ux1.corp.alleninstitute.org:8080/render-ws/v1/owner/Sharmishtaas/"
#request_url = request_url+"project/M270907_Scnn1aTg2Tdt_13/stack/%s/z/%s/box/7000,18500,1000,1000,%s/jpeg-image"%(inputStack,str(z),scale)
#request_url = request_url+"project/M270907_Scnn1aTg2Tdt_13/stack/%s/z/%s/box/3400,2900,1000,1000,%s/jpeg-image"%(inputStack,str(z),scale)
#request_url = request_url+"project/M270907_Scnn1aTg2Tdt_13/stack/%s/z/%s/box/0,0,15000,35000,%s/jpeg-image"%(inputStack,str(z),scale)
request_url = request_url+"project/M270907_Scnn1aTg2Tdt_13/stack/%s/z/%s/jpeg-image?scale=%s"%(inputStack,str(z),scale)
print (request_url)
session = requests.session()
r = session.get(request_url)
try:
img = Image.open(BytesIO(r.content))
array = numpy.asarray(img)
except:
print("Did not work!")
#print (request_url)
#boxparams=[1200,2000,4000,8600]
#img = renderapi.get_image_data(inputStack,z,boxparams,scale)
outfilename = outputDirectory + "/Section_z_" + convert(z, 4) + ".jpg"
#tifffile.imsave(outfilename,array)
im = Image.fromarray(array)
im.save(outfilename)
z = z+args.skip[0]