Analyses files for US-IALE demo planting application

blender_patches.py

# -*- coding: utf-8 -*-
"""
Created on Tue Mar 28 17:32:38 2017

@author: tangible
"""

import os
import shutil
import glob
from os.path import expanduser
from datetime import datetime
import analyses
from tangible_utils import get_environment
from experiment import updateDisplay
import grass.script as gscript
from grass.exceptions import CalledModuleError

trees = {1: "class1",
         2: "class2",
         3: "mixed",
         4: "class3",
         5: "class4"}


def run_patches(real_elev, scanned_elev, eventHandler, env, **kwargs):
    group = 'color'
    segment = 'segment'
    signature = 'signature'
    classification = 'classification'
    filtered_classification = 'fclassification'
    reject = 'reject'
    patches = 'patches'
    # detect patches
    gscript.run_command('i.superpixels.slic', group=group, output=segment, compactness=2,
                        minsize=50, env=env)
    gscript.run_command('i.smap', group=group, subgroup=group, signaturefile=signature,
                        output=classification, goodness=reject, env=env)
    percentile = float(gscript.parse_command('r.univar', flags='ge', map=reject, env=env)['percentile_90'])
    gscript.mapcalc('{new} = if({classif} < {thres}, {classif}, null())'.format(new=filtered_classification,
                                                                                classif=classification, thres=percentile), env=env)
    gscript.run_command('r.stats.quantile', base=segment, cover=filtered_classification, output=patches, env=env)
    gscript.mapcalc('{} = int({})'.format(patches + '_cell', patches), env=env)
    gscript.run_command('r.to.vect', flags='svt', input=patches + '_cell', output=patches, type='area', env=env)
    
    base_cat = 6
    #
    # r.li
    #
    indices = 'index_'
    # write config file if it doesn't exist
    rlipath = os.path.join(expanduser("~"), ".grass7", "r.li")
    configpath = os.path.join(rlipath, "patches")
    outputpath = os.path.join(rlipath, "output")    

    if not os.path.exists(configpath):
        with open(configpath, 'w') as f:
            f.write('SAMPLINGFRAME 0|0|1|1\n')
            f.write('SAMPLEAREA 0.0|0.0|1|1')
    
    results = {}
    results_list = []
    # TODO: scaling values
    gscript.mapcalc('{p2} = if({p} != {cl}, {p}, null())'.format(p2=patches + '2', p=patches, cl=base_cat), env=env)
    for index in ['patchnum', 'richness', 'mps', 'shannon', 'shape']:
        gscript.run_command('r.li.' + index, input=patches + '2', output=indices + index, config=configpath, env=env)
        with open(os.path.join(outputpath, indices + index), 'r') as f:
            results[index] = float(f.readlines()[0].strip().split('|')[-1])
            if index == 'mps':
                results[index] *= 10
            results_list.append(results[index])
    
    # update dashboard
    event = updateDisplay(value=results_list)
    eventHandler.postEvent(receiver=eventHandler.experiment_panel, event=event)        
    print results
    
    # export patches
    gscript.mapcalc('scanned_scan_int = int(transfer_dem)', env=env)
    
    env2 = get_environment(raster=patches, res=10)
    try:
        gscript.run_command('r.mask', flags='r', env=env)
    except:
        pass
    cats = gscript.read_command('r.describe', flags='1ni', map=patches + '_cell', env=env).strip()
    cats = [int(cat) for cat in cats.splitlines()]
    toexport = []
    for cat in cats:
        if cat == base_cat:
            continue
        gscript.run_command('r.mask', raster=patches + '_cell', maskcats=cat, env=env)
        gscript.run_command('r.to.vect', flags='svt', input='scanned_scan_int', output=patches + '_2d', type='area', env=env2)
        gscript.run_command('r.mask', flags='r', env=env)
        gscript.run_command('v.drape', input=patches + '_2d', output='patch_' + trees[cat], elevation='scanned_scan_int', env=env2)
        toexport.append('patch_' + trees[cat])
    send_file('empty.txt')
    export_polygons(vectors=toexport, env=env)

    
def export_polygons(vectors, env):
    time = datetime.now()
    suffix = '_{}_{}_{}'.format(time.hour, time.minute, time.second)
    outdir = '/run/user/1000/gvfs/smb-share:server=192.168.0.2,share=usiale/Watch'
    tmp_outdir = '/tmp'
    for vector in vectors:
        try:
            gscript.run_command('v.out.ogr', input=vector, lco="SHPT=POLYGONZ",
                                output=tmp_outdir + '/' + vector + suffix + '.shp', env=env)
        except CalledModuleError, e:
            print e
            
            
    for vector in vectors:
        print 'attempt to copy to Payams'
        for each in glob.glob(tmp_outdir + '/' +  vector + suffix + '.*'):
            print each
            ext = each.split('.')[-1]
            try:
                shutil.copyfile(each,  outdir + '/' + vector + suffix + '.' + ext)
            except OSError as e:
                if e.errno == 95:
                    pass


def send_file(name):
    outdir = '/run/user/1000/gvfs/smb-share:server=192.168.0.2,share=usiale/Watch'
    with open(os.path.join(outdir, name), 'w') as f:
        f.close()

config.json

{
  "taskDir": "/home/tangible/analyses/USIALE",
  "logDir": "/tmp/",
  "slides": {},
  "tasks": [
      {
      "title": "Blender patches",
      "layers": [

      ], 
      "base": "transfer_dem",
      "calibrate": false,
      "time_limit": 100000, 
      "scanning_params": {"smooth": 10, "numscans": 2, "zexag": 1},
      "analyses": "blender_patches.py", 
      "filter" : {"threshold": 2000, "debug": true},
      "single_scan": true,
      "display": {"multiple": true, "average": 2, "size": [600, 300], "position": [3150, 710],
                  "fontsize": 14, "maximum": [20, 6, 60, 2.5, 8],
                  "formatting_string": ["{:g}", "{:g}","{:.1f}","{:.2f}","{:.1f}"],
                  "title": ["Patch #", "Richness", "Mean size", "Shannon", "Shape ind." ]}
    }
  ]
}