Fix ESSI output time axis and coordinate offsets

.github/workflows/ci.yml

@@ -7,7 +7,7 @@ on:
   pull_request:
 
 jobs:
-  cli-parser-test:
+  unit-tests:
     runs-on: ubuntu-latest
 
     steps:
@@ -19,10 +19,46 @@ jobs:
         with:
           python-version: "3.11"
 
+      - name: Install MPI Runtime
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y openmpi-bin libopenmpi-dev
+
       - name: Install Test Dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install numpy scipy h5py pandas matplotlib
+          python -m pip install numpy scipy h5py pandas matplotlib mpi4py hdf5plugin
+
+      - name: Run Unit Tests
+        run: python -m unittest discover -s tests -p "test_*.py"
+
+      - name: Run MPI Fixture Conversion Test
+        env:
+          MPLCONFIGDIR: ${{ runner.temp }}/mplconfig
+        run: |
+          mkdir -p "$MPLCONFIGDIR" "$RUNNER_TEMP/convert-out"
+          mpirun -n 1 python convert.py \
+            -h5 template/h5NodeCrds.h5 \
+            --ssi tests/data/small.ssi \
+            -c template/motion_setting.csv \
+            -P "$RUNNER_TEMP/convert-out"
+          python - <<'PY'
+          import os
+          import h5py
+          import numpy as np
+
+          output_path = os.path.join(os.environ["RUNNER_TEMP"], "convert-out", "h5NodeCrds_motion.h5")
+          reference_path = "tests/data/h5NodeMotion.h5"
+
+          with h5py.File(output_path, "r") as output_h5, h5py.File(reference_path, "r") as reference_h5:
+              np.testing.assert_allclose(output_h5["acceleration"][:], reference_h5["acceleration"][:])
+              np.testing.assert_allclose(output_h5["xyz"][:], reference_h5["xyz"][:])
+              np.testing.assert_array_equal(output_h5["nodeTag"][:], reference_h5["nodeTag"][:])
+              assert output_h5["velocity"].shape == (108, 600)
+              assert output_h5["displacement"].shape == (108, 600)
 
-      - name: Run CLI Parser Test
-        run: python -m unittest tests.test_convert_cli
+              dt = float(output_h5["dt"][()])
+              tend = float(output_h5["tend"][()])
+              expected_tend = dt * (output_h5["acceleration"].shape[1] - 1)
+              assert abs(tend - expected_tend) < 1e-12
+          PY

convert.py

@@ -651,18 +651,21 @@ def write_to_hdf5_range_1d(h5_fname, gname, dname, data, mystart, myend):
     dset[mystart:myend] = data[:]
     h5file.close()
 
-def write_to_hdf5_range_2d(h5_fname, gname, dname, data, mystart, myend):
-    h5file = h5py.File(h5_fname, 'r+')
-    if gname == '/':
-        dset = h5file[dname]
+def write_to_hdf5_range_2d(h5_fname, gname, dname, data, mystart, myend):
+    h5file = h5py.File(h5_fname, 'r+')
+    if gname == '/':
+        dset = h5file[dname]
     else:
         grp = h5file[gname]
         dset = grp[dname]
 
-    #print('mystart=%d, myend=%d' %(mystart, myend))
-    dset[mystart:myend,:] = data[:,:]
-    h5file.close()
-
+    #print('mystart=%d, myend=%d' %(mystart, myend))
+    dset[mystart:myend,:] = data[:,:]
+    h5file.close()
+
+def get_flat_coord_range(coord_offset, ncoord, width=3):
+    return coord_offset * width, (coord_offset + ncoord) * width
+
 def create_hdf5_opensees(h5_fname, ncoord, tsteprange, essi_dt, gen_vel, gen_acc, gen_dis, extra_dname):
     tstep = tsteprange.step
     nstep = len(tsteprange)
@@ -717,8 +720,8 @@ 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+')    
+def create_hdf5_essi(h5_fname, ncoord, nstep, dt, gen_vel, gen_acc, gen_dis, extra_dname):
+    h5file = h5py.File(h5_fname, 'r+')    
 
     if gen_vel:
         dset = h5file.create_dataset('Velocity', (ncoord*3, nstep), dtype='f4')
@@ -727,9 +730,9 @@ def create_hdf5_essi(h5_fname, ncoord, nstep, dt, gen_vel, gen_acc, gen_dis, ext
     if gen_dis:        
         dset = h5file.create_dataset('Displacements', (ncoord*3, nstep), dtype='f4')    
 
-    timeseq = np.linspace(0, nstep*dt, nstep+1)    
-
-    h5file.create_dataset('Time', data=timeseq, dtype='i4')
+    timeseq = np.arange(nstep, dtype='f8') * dt
+
+    h5file.create_dataset('Time', data=timeseq, dtype='f8')
 
     h5file.close()
 
@@ -1438,29 +1441,30 @@ def generate_acc_dis_time(ssi_fname, coord_sys, ref_coord, user_x0, user_y0, use
             if mpi_rank != mpi_size-1:
                 comm.send(my_ncoord, dest=mpi_rank+1, tag=11) 
 
-    elif output_format == "ESSI":
-        if mpi_rank == 0:
-            create_hdf5_essi(output_fname, n_coord, nsteps, dt, gen_vel, gen_acc, gen_dis, extra_dname)    
-            # 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), my_offset, (my_offset+my_ncoord[0])*3)
-                write_to_hdf5_range_1d(output_fname, '/', extra_dname, is_boundary, 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:
+    elif output_format == "ESSI":
+        coords_start, coords_end = get_flat_coord_range(my_offset, my_ncoord[0])
+        if mpi_rank == 0:
+            create_hdf5_essi(output_fname, n_coord, nsteps, dt, gen_vel, gen_acc, gen_dis, extra_dname)    
+            # 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])   
+                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:
                     write_to_hdf5_range(output_fname, '/', 'Displacements', output_dis_all[:,tsteprange], my_offset*3, (my_offset+my_ncoord[0])*3)
                 if gen_vel:
                     write_to_hdf5_range(output_fname, '/', 'Velocity',     output_vel_all[:,tsteprange], my_offset*3, (my_offset+my_ncoord[0])*3)                
 
             if mpi_size > 1:
                 comm.send(my_ncoord, dest=1, tag=111)
-        else:
-            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), my_offset, (my_offset+my_ncoord[0])*3)
-                write_to_hdf5_range_1d(output_fname, '/', extra_dname, is_boundary, 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)
+        else:
+            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])   
+                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:
                     write_to_hdf5_range(output_fname, '/', 'Displacements', output_dis_all[:,tsteprange], my_offset*3, (my_offset+my_ncoord[0])*3)
                 if gen_vel:

tests/test_convert_fixture_data.py

@@ -0,0 +1,90 @@
+import os
+import sys
+import tempfile
+import types
+import unittest
+from pathlib import Path
+
+import h5py
+import numpy as np
+
+
+MPLCONFIGDIR = Path(tempfile.gettempdir()) / "mplconfig-convert-tests"
+MPLCONFIGDIR.mkdir(exist_ok=True)
+os.environ.setdefault("MPLCONFIGDIR", str(MPLCONFIGDIR))
+os.environ.setdefault("XDG_CACHE_HOME", tempfile.gettempdir())
+
+REPO_ROOT = Path(__file__).resolve().parents[1]
+sys.path.insert(0, str(REPO_ROOT))
+
+
+class _FakeComm:
+    def Barrier(self):
+        return None
+
+    def Allgather(self, sendbuf, recvbuf):
+        recvbuf[0][0] = sendbuf[0][0]
+
+    def send(self, *_args, **_kwargs):
+        raise AssertionError("send() should not be called in serial tests")
+
+    def recv(self, *_args, **_kwargs):
+        raise AssertionError("recv() should not be called in serial tests")
+
+
+mpi4py_stub = types.ModuleType("mpi4py")
+mpi4py_stub.MPI = types.SimpleNamespace(COMM_WORLD=_FakeComm(), INT=object())
+sys.modules.setdefault("mpi4py", mpi4py_stub)
+sys.modules.setdefault("hdf5plugin", types.ModuleType("hdf5plugin"))
+
+import convert
+
+
+class ConvertFixtureDataTests(unittest.TestCase):
+    def setUp(self):
+        convert.MPI = mpi4py_stub.MPI
+        self.sample_ssi = REPO_ROOT / "tests" / "data" / "small.ssi"
+        self.sample_h5 = REPO_ROOT / "template" / "h5NodeCrds.h5"
+        self.sample_csv = REPO_ROOT / "template" / "motion_setting.csv"
+        self.reference_output = REPO_ROOT / "tests" / "data" / "h5NodeMotion.h5"
+
+    def test_convert_h5_matches_checked_in_fixture_data(self):
+        with tempfile.TemporaryDirectory() as tmpdir:
+            ref_coord, start_t, end_t, tstep, rotate_angle, zero_motion_dir = convert.get_csv_meta(
+                str(self.sample_csv)
+            )
+
+            convert.convert_h5(
+                str(self.sample_h5),
+                str(self.sample_ssi),
+                tmpdir,
+                ref_coord,
+                start_t,
+                end_t,
+                tstep,
+                rotate_angle,
+                zero_motion_dir,
+                False,
+                0,
+                1,
+                False,
+            )
+
+            output_path = Path(tmpdir) / "h5NodeCrds_motion.h5"
+            self.assertTrue(output_path.exists(), f"Missing output file: {output_path}")
+
+            with h5py.File(output_path, "r") as output_h5, h5py.File(self.reference_output, "r") as reference_h5:
+                self.assertEqual(output_h5["velocity"].shape, (108, 600))
+                self.assertEqual(output_h5["displacement"].shape, (108, 600))
+                np.testing.assert_allclose(output_h5["acceleration"][:], reference_h5["acceleration"][:])
+                np.testing.assert_allclose(output_h5["xyz"][:], reference_h5["xyz"][:])
+                np.testing.assert_array_equal(output_h5["nodeTag"][:], reference_h5["nodeTag"][:])
+                self.assertEqual(float(output_h5["dt"][()]), float(reference_h5["dt"][()]))
+                self.assertEqual(float(output_h5["tstart"][()]), float(reference_h5["tstart"][()]))
+
+                expected_tend = float(output_h5["dt"][()]) * (output_h5["acceleration"].shape[1] - 1)
+                self.assertAlmostEqual(float(output_h5["tend"][()]), expected_tend)
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/test_convert_helpers.py

@@ -0,0 +1,54 @@
+import sys
+import tempfile
+import types
+import unittest
+from pathlib import Path
+
+import h5py
+import numpy as np
+
+
+REPO_ROOT = Path(__file__).resolve().parents[1]
+sys.path.insert(0, str(REPO_ROOT))
+
+mpi4py_stub = types.ModuleType("mpi4py")
+mpi4py_stub.MPI = types.SimpleNamespace()
+sys.modules.setdefault("mpi4py", mpi4py_stub)
+sys.modules.setdefault("hdf5plugin", types.ModuleType("hdf5plugin"))
+
+import convert
+
+
+class ConvertHelperTests(unittest.TestCase):
+    def test_get_flat_coord_range_scales_node_offsets_by_xyz_width(self):
+        self.assertEqual(convert.get_flat_coord_range(0, 2), (0, 6))
+        self.assertEqual(convert.get_flat_coord_range(2, 3), (6, 15))
+
+    def test_create_hdf5_essi_writes_float_time_axis_matching_motion_length(self):
+        with tempfile.TemporaryDirectory() as tmpdir:
+            path = Path(tmpdir) / "template.h5"
+            with h5py.File(path, "w"):
+                pass
+
+            convert.create_hdf5_essi(
+                str(path),
+                ncoord=2,
+                nstep=3,
+                dt=0.25,
+                gen_vel=True,
+                gen_acc=True,
+                gen_dis=True,
+                extra_dname="unused",
+            )
+
+            with h5py.File(path, "r") as h5file:
+                self.assertEqual(h5file["Velocity"].shape, (6, 3))
+                self.assertEqual(h5file["Accelerations"].shape, (6, 3))
+                self.assertEqual(h5file["Displacements"].shape, (6, 3))
+                self.assertEqual(h5file["Time"].shape, (3,))
+                self.assertEqual(h5file["Time"].dtype, np.dtype("float64"))
+                np.testing.assert_allclose(h5file["Time"][:], [0.0, 0.25, 0.5])
+
+
+if __name__ == "__main__":
+    unittest.main()