initial upload

utils/tomoatt_data_retrieval.py

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+# functinos for post-processing output data in h5 file
+
+import numpy
+import h5py
+
+
+def get_data_from_h5(fpath, fpath_grid, dataset_name, nr_glob, nt_glob, np_glob, ndiv_r, ndiv_t, ndiv_p, verbose=False):
+    """
+    Output arrays has one overlapping layer between adjusted subdomains.
+    This function will skip those layers and reconstruct the entire grid dataset.
+
+    fpath: path to field data file
+    fpaht_grid: path to grid data file
+    dataset_name: name of dataset in h5 file
+    nr_glob: number of grid points in r direction
+    nt_glob: number of grid points in t direction
+    np_glob: number of grid points in p direction
+    ndiv_r: number of subdomains in r direction
+    ndiv_t: number of subdomains in t direction
+    ndiv_p: number of subdomains in p direction
+    verbose: print out information
+
+    """
+    # total number of subdomains
+    n_sub = ndiv_r*ndiv_t*ndiv_p
+
+    # total points on each direction with overlap
+    nr_total_glob = nr_glob + ndiv_r - 1
+    nt_total_glob = nt_glob + ndiv_t - 1
+    np_total_glob = np_glob + ndiv_p - 1
+
+    # prepare a 3D array to store the data
+    data_glob = numpy.zeros((nr_glob,nt_glob,np_glob), dtype=numpy.float64)
+    grid_glob_r = numpy.zeros((nr_glob,nt_glob,np_glob), dtype=numpy.float64)
+    grid_glob_t = numpy.zeros((nr_glob,nt_glob,np_glob), dtype=numpy.float64)
+    grid_glob_p = numpy.zeros((nr_glob,nt_glob,np_glob), dtype=numpy.float64)
+
+    # open grid data file
+    fgrid = h5py.File(fpath_grid, 'r')
+
+    # open field data file
+    fdata = h5py.File(fpath, 'r')
+
+    #try:
+    # load data data by each subdomain
+
+    # offset
+    offset = 0
+
+    for ir_sub in range(ndiv_r):
+        for it_sub in range(ndiv_t):
+            for ip_sub in range(ndiv_p):
+
+                # number of data point for this sub domain
+                nr_sub = nr_glob//ndiv_r
+                nt_sub = nt_glob//ndiv_t
+                np_sub = np_glob//ndiv_p
+
+                # offset for each direction
+                offset_r = ir_sub*nr_sub
+                offset_t = it_sub*nt_sub
+                offset_p = ip_sub*np_sub
+
+                # add modulus to the last subdomains
+                if ir_sub == ndiv_r-1:
+                    nr_sub += nr_glob%ndiv_r
+                if it_sub == ndiv_t-1:
+                    nt_sub += nt_glob%ndiv_t
+                if ip_sub == ndiv_p-1:
+                    np_sub += np_glob%ndiv_p
+
+                # add overlap layer if this subdomain is not the last one for each direction
+                if ir_sub != ndiv_r-1:
+                    nr_sub += 1
+                if it_sub != ndiv_t-1:
+                    nt_sub += 1
+                if ip_sub != ndiv_p-1:
+                    np_sub += 1
+
+                # number of data point for this sub domain
+                n_points_total_sub = nr_sub*nt_sub*np_sub
+
+                # load data
+                data_sub = fdata[dataset_name][offset:offset+n_points_total_sub]
+                data_sub_p = fgrid["/Mesh/node_coords_p"][offset:offset+n_points_total_sub]
+                data_sub_t = fgrid["/Mesh/node_coords_t"][offset:offset+n_points_total_sub]
+                data_sub_r = fgrid["/Mesh/node_coords_r"][offset:offset+n_points_total_sub]
+
+                # reshape data
+                data_sub = data_sub.reshape(nr_sub, nt_sub, np_sub)
+                data_sub_p = data_sub_p.reshape(nr_sub, nt_sub, np_sub)
+                data_sub_t = data_sub_t.reshape(nr_sub, nt_sub, np_sub)
+                data_sub_r = data_sub_r.reshape(nr_sub, nt_sub, np_sub)
+
+
+                # put those data in global 3d array
+                data_glob[offset_r:offset_r+nr_sub, offset_t:offset_t+nt_sub, offset_p:offset_p+np_sub] = data_sub
+                grid_glob_p[offset_r:offset_r+nr_sub, offset_t:offset_t+nt_sub, offset_p:offset_p+np_sub] = data_sub_p
+                grid_glob_t[offset_r:offset_r+nr_sub, offset_t:offset_t+nt_sub, offset_p:offset_p+np_sub] = data_sub_t
+                grid_glob_r[offset_r:offset_r+nr_sub, offset_t:offset_t+nt_sub, offset_p:offset_p+np_sub] = data_sub_r
+
+                # update offset
+                offset += n_points_total_sub
+
+
+    return data_glob, grid_glob_r, grid_glob_t, grid_glob_p
+
+    #except:
+    #    fdata.close()
+    #    fgrid.close()
+    #    print("error occured while reading file.")
+
+    #    return -1
+
+
+# output arrays has one overlapping layer between adjusted subdomains
+# this function will skip those layers and reconstruct the entire grid dataset
+def get_data_from_ascii(fpath, fpath_grid, nr_glob, nt_glob, np_glob, ndiv_r, ndiv_t, ndiv_p, verbose=False):
+    """
+
+    fpath: path to ascii data file
+    fpath_grid: path to ascii grid data file
+    nr_glob: number of grid points in r direction
+    nt_glob: number of grid points in t direction
+    np_glob: number of grid points in p direction
+    ndiv_r: number of subdomains in r direction
+    ndiv_t: number of subdomains in t direction
+    ndiv_p: number of subdomains in p direction
+    verbose: print out information
+
+    """
+    # total number of subdomains
+    n_sub = ndiv_r*ndiv_t*ndiv_p
+
+    # total points on each direction with overlap
+    nr_total_glob = nr_glob + ndiv_r - 1
+    nt_total_glob = nt_glob + ndiv_t - 1
+    np_total_glob = np_glob + ndiv_p - 1
+
+    # prepare a 3D array to store the data
+    data_glob = numpy.zeros((nr_glob,nt_glob,np_glob), dtype=numpy.float64)
+    grid_glob_r = numpy.zeros((nr_glob,nt_glob,np_glob), dtype=numpy.float64)
+    grid_glob_t = numpy.zeros((nr_glob,nt_glob,np_glob), dtype=numpy.float64)
+    grid_glob_p = numpy.zeros((nr_glob,nt_glob,np_glob), dtype=numpy.float64)
+
+    # read data
+    data_tmp = numpy.loadtxt(fpath)
+    grid_tmp = numpy.loadtxt(fpath_grid)
+
+    # load data data by each subdomain
+
+    # offset
+    offset = 0
+
+    for ir_sub in range(ndiv_r):
+        for it_sub in range(ndiv_t):
+            for ip_sub in range(ndiv_p):
+
+                # number of data point for this sub domain
+                nr_sub = nr_glob//ndiv_r
+                nt_sub = nt_glob//ndiv_t
+                np_sub = np_glob//ndiv_p
+
+                # offset for each direction
+                offset_r = ir_sub*nr_sub
+                offset_t = it_sub*nt_sub
+                offset_p = ip_sub*np_sub
+
+                # add modulus to the last subdomains
+                if ir_sub == ndiv_r-1:
+                    nr_sub += nr_glob%ndiv_r
+                if it_sub == ndiv_t-1:
+                    nt_sub += nt_glob%ndiv_t
+                if ip_sub == ndiv_p-1:
+                    np_sub += np_glob%ndiv_p
+
+                # add overlap layer if this subdomain is not the last one for each direction
+                if ir_sub != ndiv_r-1:
+                    nr_sub += 1
+                if it_sub != ndiv_t-1:
+                    nt_sub += 1
+                if ip_sub != ndiv_p-1:
+                    np_sub += 1
+
+                # number of data point for this sub domain
+                n_points_total_sub = nr_sub*nt_sub*np_sub
+
+                # load data
+                data_sub = data_tmp[offset:offset+n_points_total_sub]
+                grid_sub_p = grid_tmp[offset:offset+n_points_total_sub,0]
+                grid_sub_t = grid_tmp[offset:offset+n_points_total_sub,1]
+                grid_sub_r = grid_tmp[offset:offset+n_points_total_sub,2]
+
+                # reshape data
+                data_sub = data_sub.reshape(nr_sub, nt_sub, np_sub)
+                grid_sub_p = grid_sub_p.reshape(nr_sub, nt_sub, np_sub)
+                grid_sub_t = grid_sub_t.reshape(nr_sub, nt_sub, np_sub)
+                grid_sub_r = grid_sub_r.reshape(nr_sub, nt_sub, np_sub)
+
+                # put those data in global 3d array
+                data_glob[offset_r:offset_r+nr_sub, offset_t:offset_t+nt_sub, offset_p:offset_p+np_sub] = data_sub
+                grid_glob_p[offset_r:offset_r+nr_sub, offset_t:offset_t+nt_sub, offset_p:offset_p+np_sub] = grid_sub_p
+                grid_glob_t[offset_r:offset_r+nr_sub, offset_t:offset_t+nt_sub, offset_p:offset_p+np_sub] = grid_sub_t
+                grid_glob_r[offset_r:offset_r+nr_sub, offset_t:offset_t+nt_sub, offset_p:offset_p+np_sub] = grid_sub_r
+
+                # update offset
+                offset += n_points_total_sub
+
+
+    return data_glob, grid_glob_r, grid_glob_t, grid_glob_p
+
+
+
+
+
+
+if __name__ == '__main__':
+
+    # examples
+    fpath = './OUTPUT_FILES/out_data_sim_0.h5'
+    fpath_grid = './OUPUT_FILES/out_data_grid.h5'
+    nr = 10
+    nt = 10
+    np = 10
+    ndiv_r = 2
+    ndiv_t = 2
+    ndiv_p = 2
+    Ks_tomoatt = get_data_from_h5(fpath, fpath_grid, "Data/Ks_inv_0000", nr, nt, np, ndiv_r, ndiv_t, ndiv_p, verbose=True)