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Merged
houjun merged 6 commits into from
Apr 21, 2026
Merged

Fix CI for expanded output format support #10

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0ef835c
Sync to include recent updates
jf-huang Jan 10, 2025
b29152e
Sync to include recent updates
jf-huang Jan 30, 2025
5176238
Switch on opensees & essi output format for csv & h5 input kinds
Apr 20, 2026
988c39b
Fix CI for expanded output format support
houjun Apr 21, 2026
99bacc0
Address PR review feedback
houjun Apr 21, 2026
76d9ffc
Reduce formatting-only PR diff noise
houjun Apr 21, 2026
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4 changes: 2 additions & 2 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -53,8 +53,8 @@ When `--output-format` is omitted, the script keeps the current default for each
Notes:
- `--timerange start end step` is in SSI time units.
- If `start == end`, the script keeps all steps from `start` to the end of the SSI record.
- `--output-format point` is supported for DRM, HDF5, CSV, and template-driven inputs.
- `--output-format opensees` and `--output-format essi` require input that carries boundary-node metadata, so they are only supported for DRM or template-driven inputs.
- `--output-format point`, `--output-format opensees`, and `--output-format essi` are supported for DRM, HDF5, CSV, and template-driven inputs.
- HDF5 and CSV inputs keep their `nodeTag` metadata when writing OpenSees or ESSI-style outputs.

## Examples

Expand Down
66 changes: 41 additions & 25 deletions convert.py
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Original file line number Diff line number Diff line change
Expand Up @@ -75,8 +75,8 @@ def resolve_output_mode(input_kind, requested_output_mode):
}
supported = {
'drm': {'point', 'opensees', 'essi'},
'h5': {'point'},
'csv': {'point'},
'h5': {'point', 'opensees', 'essi'},
'csv': {'point', 'opensees', 'essi'},
'template': {'point', 'opensees', 'essi'},
}

Expand Down Expand Up @@ -112,7 +112,10 @@ def get_output_filename(input_kind, output_mode, save_path, source_fname, explic
if output_mode == 'essi':
if input_kind == 'template' and not explicit_output_mode:
return source_fname
return os.path.join(save_path, os.path.basename(source_fname))
output_name = os.path.basename(source_fname)
if input_kind == 'csv':
output_name = f'{os.path.splitext(output_name)[0]}.h5'
return os.path.join(save_path, output_name)

raise ValueError(f'Unsupported output format: {output_mode}')

Expand Down Expand Up @@ -786,7 +789,20 @@ def create_hdf5_csv(h5_fname, ncoord, tsteprange, essi_dt, gen_vel, gen_acc, gen
h5file.close()

def create_hdf5_essi(h5_fname, ncoord, nstep, dt, gen_vel, gen_acc, gen_dis, extra_dname):
h5file = h5py.File(h5_fname, 'r+')
h5file = h5py.File(h5_fname, 'a')

coord_shape = (ncoord * 3,)
meta_shape = (ncoord,)

if 'Coordinates' in h5file and h5file['Coordinates'].shape != coord_shape:
del h5file['Coordinates']
if 'Coordinates' not in h5file:
h5file.create_dataset('Coordinates', coord_shape, dtype='f8')

if extra_dname in h5file and h5file[extra_dname].shape != meta_shape:
del h5file[extra_dname]
if extra_dname not in h5file:
h5file.create_dataset(extra_dname, meta_shape, dtype='i4')

for dname in ('Velocity', 'Accelerations', 'Displacements', 'Time'):
if dname in h5file:
Expand Down Expand Up @@ -947,7 +963,7 @@ def linear_interp(data_dict, x, y, z):
result = ((c000 * (1-xd) + c100 * xd) * (1-yd) + (c010 * (1-xd) + c110 * xd) * yd) * (1-zd) + ((c001 * (1-xd) + c101 * xd) * (1-yd) + (c011 * (1-xd) + c111 * xd) * yd) * zd
return result

def generate_acc_dis_time(ssi_fname, coord_sys, ref_coord, user_x0, user_y0, user_z0, n_coord, start_t, end_t, tstep, rotate_angle, zeroMotionDir, gen_vel, gen_acc, gen_dis, verbose, plot_only, output_fname, mpi_rank, mpi_size, extra_data, extra_dname, output_format):
def generate_acc_dis_time(ssi_fname, coord_sys, ref_coord, user_x0, user_y0, user_z0, n_coord, start_t, end_t, tstep, rotate_angle, zeroMotionDir, gen_vel, gen_acc, gen_dis, verbose, plot_only, output_fname, mpi_rank, mpi_size, extra_values_input, extra_dname, output_format):
if zeroMotionDir is None or pd.isna(zeroMotionDir):
zeroMotionDir = 'None'
elif isinstance(zeroMotionDir, str):
Expand Down Expand Up @@ -1166,7 +1182,7 @@ def generate_acc_dis_time(ssi_fname, coord_sys, ref_coord, user_x0, user_y0, use
read_coords_vel_1 = {}
read_coords_vel_2 = {}
# coords_str_dict = {}
is_boundary = np.zeros(n_coord, dtype='i4')
extra_values = np.zeros(n_coord, dtype='i4')
my_ncoord = np.zeros(1, dtype='int')
my_user_coordinates = np.zeros((n_coord,3), dtype='f8')
my_converted_coordinates = np.zeros((n_coord,3), dtype='f8')
Expand Down Expand Up @@ -1224,7 +1240,7 @@ def generate_acc_dis_time(ssi_fname, coord_sys, ref_coord, user_x0, user_y0, use
else:
my_cids_dict[cid] = {coord_str}

is_boundary[my_ncoord[0]] = extra_data[i]
extra_values[my_ncoord[0]] = extra_values_input[i]
my_ncoord[0] += 1
#end if assigned to my rank
#end for i in all coordinates
Expand All @@ -1235,7 +1251,7 @@ def generate_acc_dis_time(ssi_fname, coord_sys, ref_coord, user_x0, user_y0, use
# Allocated more than needed previously, resize here
my_user_coordinates.resize(my_ncoord[0], 3)
my_converted_coordinates.resize(my_ncoord[0], 3)
is_boundary.resize(my_ncoord[0])
extra_values.resize(my_ncoord[0])

# if mpi_rank == 0:
# # print('read_coords_vel_0 =', read_coords_vel_0)
Expand Down Expand Up @@ -1452,7 +1468,7 @@ def generate_acc_dis_time(ssi_fname, coord_sys, ref_coord, user_x0, user_y0, use

if my_ncoord[0] > 0:
write_to_hdf5_range_2d(output_fname, 'DRM_Data', 'xyz', my_user_coordinates, my_offset, (my_offset+my_ncoord[0]))
write_to_hdf5_range_1d(output_fname, 'DRM_Data', extra_dname, is_boundary, my_offset, my_offset+my_ncoord[0])
write_to_hdf5_range_1d(output_fname, 'DRM_Data', extra_dname, extra_values, my_offset, my_offset+my_ncoord[0])
if gen_acc:
write_to_hdf5_range(output_fname, 'DRM_Data', 'acceleration', output_acc_all[:,tsteprange], my_offset*3, (my_offset+my_ncoord[0])*3)
if gen_dis:
Expand All @@ -1467,7 +1483,7 @@ def generate_acc_dis_time(ssi_fname, coord_sys, ref_coord, user_x0, user_y0, use
if verbose:
print('Rank', mpi_rank, 'start to write data')
write_to_hdf5_range_2d(output_fname, 'DRM_Data', 'xyz', my_user_coordinates, my_offset, (my_offset+my_ncoord[0]))
write_to_hdf5_range_1d(output_fname, 'DRM_Data', extra_dname, is_boundary, my_offset, my_offset+my_ncoord[0])
write_to_hdf5_range_1d(output_fname, 'DRM_Data', extra_dname, extra_values, my_offset, my_offset+my_ncoord[0])

if gen_acc:
write_to_hdf5_range(output_fname, 'DRM_Data', 'acceleration', output_acc_all[:,tsteprange], my_offset*3, (my_offset+my_ncoord[0])*3)
Expand All @@ -1484,7 +1500,7 @@ def generate_acc_dis_time(ssi_fname, coord_sys, ref_coord, user_x0, user_y0, use

if my_ncoord[0] > 0:
write_to_hdf5_range_2d(output_fname, '/', 'xyz', my_user_coordinates, my_offset, (my_offset+my_ncoord[0]))
write_to_hdf5_range_1d(output_fname, '/', extra_dname, is_boundary, my_offset, my_offset+my_ncoord[0])
write_to_hdf5_range_1d(output_fname, '/', extra_dname, extra_values, my_offset, my_offset+my_ncoord[0])
if gen_acc:
write_to_hdf5_range(output_fname, '/', 'acceleration', output_acc_all[:,tsteprange], my_offset*3, (my_offset+my_ncoord[0])*3)
if gen_dis:
Expand All @@ -1499,7 +1515,7 @@ def generate_acc_dis_time(ssi_fname, coord_sys, ref_coord, user_x0, user_y0, use
if verbose:
print('Rank', mpi_rank, 'start to write data')
write_to_hdf5_range_2d(output_fname, '/', 'xyz', my_user_coordinates, my_offset, (my_offset+my_ncoord[0]))
write_to_hdf5_range_1d(output_fname, '/', extra_dname, is_boundary, my_offset, my_offset+my_ncoord[0])
write_to_hdf5_range_1d(output_fname, '/', extra_dname, extra_values, my_offset, my_offset+my_ncoord[0])

if gen_acc:
write_to_hdf5_range(output_fname, '/', 'acceleration', output_acc_all[:,tsteprange], my_offset*3, (my_offset+my_ncoord[0])*3)
Expand All @@ -1517,7 +1533,7 @@ def generate_acc_dis_time(ssi_fname, coord_sys, ref_coord, user_x0, user_y0, use
# Write to the template file
if my_ncoord[0] > 0:
write_to_hdf5_range_1d(output_fname, '/', 'Coordinates', my_user_coordinates.reshape(my_ncoord[0]*3), coords_start, coords_end)
write_to_hdf5_range_1d(output_fname, '/', extra_dname, is_boundary, my_offset, my_offset+my_ncoord[0])
write_to_hdf5_range_1d(output_fname, '/', extra_dname, extra_values, my_offset, my_offset+my_ncoord[0])
if gen_acc:
write_to_hdf5_range(output_fname, '/', 'Accelerations', output_acc_all[:,tsteprange], my_offset*3, (my_offset+my_ncoord[0])*3)
if gen_dis:
Expand All @@ -1531,7 +1547,7 @@ def generate_acc_dis_time(ssi_fname, coord_sys, ref_coord, user_x0, user_y0, use
data = comm.recv(source=mpi_rank-1, tag=111)
if my_ncoord[0] > 0:
write_to_hdf5_range_1d(output_fname, '/', 'Coordinates', my_user_coordinates.reshape(my_ncoord[0]*3), coords_start, coords_end)
write_to_hdf5_range_1d(output_fname, '/', extra_dname, is_boundary, my_offset, my_offset+my_ncoord[0])
write_to_hdf5_range_1d(output_fname, '/', extra_dname, extra_values, my_offset, my_offset+my_ncoord[0])
if gen_acc:
write_to_hdf5_range(output_fname, '/', 'Accelerations', output_acc_all[:,tsteprange], my_offset*3, (my_offset+my_ncoord[0])*3)
if gen_dis:
Expand Down Expand Up @@ -1559,8 +1575,8 @@ def convert_drm(drm_fname, ssi_fname, save_path, ref_coord, start_t, end_t, tste
output_format = resolve_output_mode('drm', requested_output_mode)

# original unrotated node coordinates
user_x0, user_y0, user_z0, n_coord, isboundary = read_coord_drm(drm_fname, verbose)
isboundary = np.asarray(isboundary).reshape(-1)
user_x0, user_y0, user_z0, n_coord, boundary_flags = read_coord_drm(drm_fname, verbose)
extra_values = np.asarray(boundary_flags).reshape(-1)
if verbose and mpi_rank == 0:
print('Done read %d coordinates, first is (%d, %d, %d), last is (%d, %d, %d)' % (n_coord, user_x0[0], user_y0[0], user_z0[0], user_x0[-1], user_y0[-1], user_z0[-1]))
print('x, y, z (min/max): (%.0f, %.0f), (%.0f, %.0f), (%.0f, %.0f)' % (np.min(user_x0), np.max(user_x0), np.min(user_y0), np.max(user_y0), np.min(user_z0), np.max(user_z0)) )
Expand All @@ -1584,7 +1600,7 @@ def convert_drm(drm_fname, ssi_fname, save_path, ref_coord, start_t, end_t, tste
prepare_essi_output_file(drm_fname, output_fname)
MPI.COMM_WORLD.Barrier()

generate_acc_dis_time(ssi_fname, coord_sys, ref_coord, user_x0, user_y0, user_z0, n_coord, start_t, end_t, tstep, rotate_angle, zeroMotionDir,gen_vel, gen_acc, gen_dis, verbose, plot_only, output_fname, mpi_rank, mpi_size, isboundary, extra_dname, output_format)
generate_acc_dis_time(ssi_fname, coord_sys, ref_coord, user_x0, user_y0, user_z0, n_coord, start_t, end_t, tstep, rotate_angle, zeroMotionDir,gen_vel, gen_acc, gen_dis, verbose, plot_only, output_fname, mpi_rank, mpi_size, extra_values, extra_dname, output_format)

return

Expand All @@ -1595,7 +1611,7 @@ def convert_h5(h5_fname, ssi_fname, save_path, ref_coord, start_t, end_t, tstep,

coord_sys = ['y', 'x', '-z']
output_format = resolve_output_mode('h5', requested_output_mode)
gen_vel = True
gen_vel = output_format != 'opensees'
gen_dis = True
gen_acc = True
extra_dname = 'nodeTag'
Expand All @@ -1622,7 +1638,7 @@ def convert_csv(csv_fname, ssi_fname, save_path, ref_coord, start_t, end_t, tste

coord_sys = ['y', 'x', '-z']
output_format = resolve_output_mode('csv', requested_output_mode)
gen_vel = True
gen_vel = output_format != 'opensees'
gen_dis = True
gen_acc = True
extra_dname = 'nodeTag'
Expand All @@ -1631,9 +1647,9 @@ def convert_csv(csv_fname, ssi_fname, save_path, ref_coord, start_t, end_t, tste
df = pd.read_csv(csv_fname)
node_tags = df['nodeTag'][:].tolist()
n_coord = len(node_tags)
user_x0 = np.zeros(n_coord, dtype='f4')
user_y0 = np.zeros(n_coord, dtype='f4')
user_z0 = np.zeros(n_coord, dtype='f4')
user_x0 = np.zeros(n_coord, dtype='f8')
user_y0 = np.zeros(n_coord, dtype='f8')
user_z0 = np.zeros(n_coord, dtype='f8')
for i in range(0, n_coord):
user_x0[i] = df.loc[i, 'x']
user_y0[i] = df.loc[i, 'y']
Expand Down Expand Up @@ -1699,8 +1715,8 @@ def convert_template(csv_fname, template_fname, ssi_fname, start_t, end_t, tstep
template_file = h5py.File(template_fname)
coordinates = template_file['Coordinates'][:]

is_boundary = np.asarray(template_file['Is Boundary Node'][:]).reshape(-1)
n_coord = len(is_boundary)
extra_values = np.asarray(template_file['Is Boundary Node'][:]).reshape(-1)
n_coord = len(extra_values)
user_x = np.zeros(n_coord)
user_y = np.zeros(n_coord)
user_z = np.zeros(n_coord)
Expand All @@ -1724,7 +1740,7 @@ def convert_template(csv_fname, template_fname, ssi_fname, start_t, end_t, tstep
prepare_essi_output_file(template_fname, output_fname)
MPI.COMM_WORLD.Barrier()

generate_acc_dis_time(ssi_fname, coord_sys, ref_coord, user_x, user_y, user_z, n_coord, start_t, end_t, tstep, rotate_angle, zeroMotionDir, gen_vel, gen_acc, gen_dis, verbose, plot_only, output_fname, mpi_rank, mpi_size, is_boundary, extra_dname, output_format)
generate_acc_dis_time(ssi_fname, coord_sys, ref_coord, user_x, user_y, user_z, n_coord, start_t, end_t, tstep, rotate_angle, zeroMotionDir, gen_vel, gen_acc, gen_dis, verbose, plot_only, output_fname, mpi_rank, mpi_size, extra_values, extra_dname, output_format)
return

if __name__ == "__main__":
Expand Down
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