if __name__ == "__main__" and __package__ is None:

__package__ = "renderapps.materialize.make_downsample_image_stack"

import json

import os

import renderapi

from ..module.render_module import RenderModule,RenderParameters

from json_module import InputFile,InputDir,OutputDir

import marshmallow as mm

from functools import partial

import glob

import time

import numpy as np

import time

from PIL import Image

import tifffile

from functools import reduce

import operator

#modified and fixed by Sharmishtaa Seshamani

example_parameters={

"render":{

"host":"ibs-forrestc-ux1",

"port":80,

"client_scripts":"/var/www/render/render-ws-java-client/src/main/scripts",

"owner":"S3_Run1",

"project":"S3_Run1_Jarvis"

},

"input_stacks": "Stitched_DAPI_1_Lowres_68_to_112_RoughAlign_filter1_round1111_0_156,Stitched_DAPI_1_Lowres_68_to_112_RoughAlign_filter1_round1111_157_187,Stitched_DAPI_1_Lowres_68_to_112_RoughAlign_filter1_round1111_188_694",

"input_projects": "S3_Run1_Jarvis,S3_Run1_Jarvis,S3_Run1_Jarvis",

"output_project": "S3_Run1_Jarvis",

'output_stack':'Stitched_DAPI_1_Lowres_68_to_223_RoughAlign_filter1_round1111_concat',

"output_directory":"/nas4/data/S3_Run1_Jarvis/processed/tilespecs_for_concat_roughalign",

"adjust_z": True,

'pool_size':20

}

class ConcatenateStacksParameters(RenderParameters):

input_stacks = mm.fields.Str(required=True,

metadata={'description':'input stacks'})

input_projects = mm.fields.Str(required=True,

metadata={'description':'input projects '})

output_stack = mm.fields.Str(required=True,

metadata={'description':'output stack to name'})

output_project = mm.fields.Str(required=True,

metadata={'description':'output project'})

output_directory = mm.fields.Str(required=True,

metadata={'description':'input stacks'})

pool_size = mm.fields.Int(required=False,default=20,

metadata={'description':'number of parallel threads to use'})

adjust_z = mm.fields.Bool(required=False,default=False,

metadata={'description':'whether to adjust z values'})

def process_z(stack,project,render,output_directory,z):

print(z)

tilespecs = renderapi.tilespec.get_tile_specs_from_z(stack,z,render=render,project=project)

tilespecfilename = os.path.join(output_directory,'tilespec_%04d.json'%z)

print(tilespecfilename)

fp = open(tilespecfilename,'w')

json.dump([ts.to_dict() for ts in tilespecs] ,fp,indent=4)

fp.close()

def process_z_adjust(stack,project,render,output_directory,Z):

print(Z[0])

tilespecs = renderapi.tilespec.get_tile_specs_from_z(stack,Z[0],render=render,project=project)

for ts in tilespecs:

d = ts.to_dict()

d['z'] = Z[1]

ts.from_dict(d)

tilespecfilename = os.path.join(output_directory,'tilespec_%04d.json'%Z[1])

print(tilespecfilename)

fp = open(tilespecfilename,'w')

json.dump([ts.to_dict() for ts in tilespecs] ,fp,indent=4)

fp.close()

class ConcatenateStacks(RenderModule):

def __init__(self,schema_type=None,*args,**kwargs):

if schema_type is None:

schema_type = ConcatenateStacksParameters

super(ConcatenateStacks,self).__init__(schema_type=schema_type,*args,**kwargs)

def run(self):

i_st = self.args['input_stacks'].split(',')

i_pr = self.args['input_projects'].split(',')

render=self.render

tsarray = []

lastz = -1;

if not os.path.exists(self.args['output_directory']):

os.mkdir(self.args['output_directory'])

for i in range(0,len(i_st)):

print(i)

outstack = self.args['output_stack']+str(i)

outproject = self.args['output_project']

self.render.run(renderapi.stack.clone_stack,i_st[i],outstack,toProject=outproject,project=i_pr[i])

z = self.render.run(renderapi.stack.get_z_values_for_stack,outstack, project = outproject)

if self.args['adjust_z'] == True:

newz = range(lastz+1,lastz+1+len(z))

Z = []

for i in range(0,len(z)):

Z.append([z[i],newz[i]])

mypartial = partial(process_z_adjust,outstack,outproject,render,self.args['output_directory'])

with renderapi.client.WithPool(self.args['pool_size']) as pool:

pool.map(mypartial,Z)

lastz = newz[len(newz)-1]

else:

mypartial = partial(process_z,outstack,outproject,render,self.args['output_directory'])

with renderapi.client.WithPool(self.args['pool_size']) as pool:

pool.map(mypartial,z)

print(self.args['adjust_z'])

outstack = self.args['output_stack']

jsonfiles = glob.glob("%s/*.json"%self.args['output_directory'])

renderapi.stack.create_stack(outstack,render=self.render,cycleNumber=10,cycleStepNumber=1,project=outproject)

renderapi.client.import_jsonfiles_parallel(outstack,jsonfiles,render=self.render,project=outproject)

if __name__ == "__main__":

#mod = ConcatenateStacks(input_data=example_parameters)

mod = ConcatenateStacks(schema_type=ConcatenateStacksParameters)

mod.run()