swapped orbital fit correction to script 2 as it is causing memory er…

…rors with script 1

pyrate/nci/run_pyrate_pypar.py

@@ -4,14 +4,13 @@
 import os
 from os.path import join
 import sys
-from collections import namedtuple, Counter
+from collections import namedtuple
 from operator import itemgetter
 import numpy as np
 from osgeo import gdal
 
 from pyrate import config as cf
 from pyrate import mst
-from pyrate import orbital
 from pyrate import refpixel
 from pyrate import remove_aps_delay as aps
 from pyrate import shared
@@ -118,26 +117,6 @@ def main(params, config_file=sys.argv[1]):
         for i in ifgs:
             i.close()
 
-    parallel.barrier()
-
-    orb_fit_calc_mpi(dest_tifs, parallel, params)
-
-    parallel.barrier()
-    output_dir = params[cf.OUT_DIR]
-    # save phase data and phase_sum used in the reference phase estimation
-    if rank == MASTER_PROCESS:
-        phase_sum = 0
-        for d in dest_tifs:
-            ifg = shared.Ifg(d)
-            ifg.open()
-            ifg.nodata_value = params[cf.NO_DATA_VALUE]
-            phase_sum += ifg.phase_data
-            ifg.save_numpy_phase(numpy_file=os.path.join(
-                output_dir, os.path.basename(d).split('.')[0] + '.npy'))
-            ifg.close()
-        comp = np.isnan(phase_sum)  # this is the same as in Matlab
-        comp = np.ravel(comp, order='F')  # this is the same as in Matlab
-        np.save(file=os.path.join(output_dir, 'comp.npy'), arr=comp)
     parallel.finalize()
 
 
@@ -187,21 +166,6 @@ def convert_phase_to_numpy(dest_tifs, output_dir, tiles, parallel):
     return preread_ifgs
 
 
-def orb_fit_calc_mpi(ifg_paths, parallel, params):
-    print 'calculating orbfit correction'
-    if params[cf.ORBITAL_FIT_METHOD] != 1:
-        raise cf.ConfigException('For now orbfit method must be 1')
-
-    # ifgs = shared.prepare_ifgs_without_phase(ifg_paths, params)
-    no_ifgs = len(ifg_paths)
-    process_indices = parallel.calc_indices(no_ifgs)
-    process_ifgs = [itemgetter(p)(ifg_paths) for p in process_indices]
-
-    mlooked = None
-    # TODO: MPI orbfit method 2
-    orbital.orbital_correction(process_ifgs, params, mlooked=mlooked)
-
-
 def ref_pixel_calc_mpi(MPI_myID, ifg_paths, num_processors, parallel, params):
     half_patch_size, thresh, grid = refpixel.ref_pixel_setup(ifg_paths, params)
 

pyrate/nci/run_pyrate_pypar_2.py

@@ -14,6 +14,7 @@
 from pyrate.nci.parallel import Parallel
 from pyrate.scripts import run_pyrate
 from pyrate.scripts.run_pyrate import write_msg
+from pyrate import orbital
 gdal.SetCacheMax(64)
 
 __author__ = 'sudipta'
@@ -39,6 +40,26 @@ def main(params, config_file=sys.argv[1]):
     refpx, refpy = np.load(ref_pixel_file)
     print 'Found reference pixel', refpx, refpy
 
+    orb_fit_calc_mpi(dest_tifs, parallel, params)
+
+    parallel.barrier()
+    output_dir = params[cf.OUT_DIR]
+
+    # save phase data and phase_sum used in the reference phase estimation
+    if rank == MASTER_PROCESS:
+        phase_sum = 0
+        for d in dest_tifs:
+            ifg = shared.Ifg(d)
+            ifg.open()
+            ifg.nodata_value = params[cf.NO_DATA_VALUE]
+            phase_sum += ifg.phase_data
+            ifg.save_numpy_phase(numpy_file=os.path.join(
+                output_dir, os.path.basename(d).split('.')[0] + '.npy'))
+            ifg.close()
+        comp = np.isnan(phase_sum)  # this is the same as in Matlab
+        comp = np.ravel(comp, order='F')  # this is the same as in Matlab
+        np.save(file=os.path.join(output_dir, 'comp.npy'), arr=comp)
+
     parallel.barrier()
     # estimate and remove reference phase
     ref_phase_estimation_mpi(rank, dest_tifs, parallel, params, refpx, refpy)
@@ -174,6 +195,22 @@ def maxvar_vcm_mpi(rank, ifg_paths, parallel, params):
     return maxvar, vcmt
 
 
+def orb_fit_calc_mpi(ifg_paths, parallel, params):
+    print 'calculating orbfit correction'
+    if params[cf.ORBITAL_FIT_METHOD] != 1:
+        raise cf.ConfigException('For now orbfit method must be 1')
+
+    # ifgs = shared.prepare_ifgs_without_phase(ifg_paths, params)
+    no_ifgs = len(ifg_paths)
+    process_indices = parallel.calc_indices(no_ifgs)
+    process_ifgs = [itemgetter(p)(ifg_paths) for p in process_indices]
+
+    mlooked = None
+    # TODO: MPI orbfit method 2
+    orbital.orbital_correction(process_ifgs, params, mlooked=mlooked)
+    print 'finished orbfit calculation for process {}'.format(parallel.rank)
+
+
 if __name__ == '__main__':
     # read in the config file, and params for the simulation
     params = run_pyrate.get_ifg_paths()[2]