mode sources and monitors work with conversion

flexcompute · Oct 21, 2021 · 7cec00c · 7cec00c
1 parent d076eb5
commit 7cec00c
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Showing 11 changed files with 445 additions and 672 deletions.
diff --git a/README.md b/README.md
@@ -188,9 +188,6 @@ https://www.atlassian.com/git/tutorials/merging-vs-rebasing
 - [x] Simplify MonitorData
     - [x] remove MonitorData.monitor  and MonitorData.monitor_name attributes.
     - [x] remove MonitorData.load() and MonitorData.export()
-    - [ ] assert all SimulationData.monitor_data.keys() are in SimulationData.simulation.monitor.keys() <- not necessry.
-    - [ ] provide optional args to SimulationData.export() to only export some MonitorData by key <- not necessary?
-    - [ ] Move any interfaces in MonitorData to SimulationData (geometry, plotting, etc).
     - [x] Make monitordata.load_from_group aware of lists
 - [x] Use shapely for geometry ops / plotting?  `Geometry.geo(x=0)` -> shapely representation.
 	- [x] Fix all tests.
@@ -208,12 +205,13 @@ https://www.atlassian.com/git/tutorials/merging-vs-rebasing
 - [ ] Handle Inf as it's own keyword that depends on simulation bounds.
 - [ ] Make Uniform Samplers separate classes? (dont evaluate / store freqs, times)?
 - [ ] setup.cfg for installing packages with more granularity (base, docs, tests)
+- [ ] Move any interfaces in MonitorData to SimulationData (geometry, plotting, etc).
 
 
 #### Requires some focused time
 - [ ] Nail down simulationData interfaces for plotting.
 - [ ] Figue out webAPI running progress issues. (can we get separate status for time-stepping?)
-- [ ] **Conversion for mode monitors / mode sources.**
+- [x] Conversion for mode monitors / mode sources.
 - [ ] Get near2far working correctly.
 - [ ] Use mode solver for the relevant example notebooks.
 - [ ] Document everything fully.

diff --git a/notebooks/Modal_sources_monitors.ipynb b/notebooks/Modal_sources_monitors.ipynb
diff --git a/notebooks/data/mode_converter.hdf5 b/notebooks/data/mode_converter.hdf5
diff --git a/notebooks/data/simulation.hdf5 b/notebooks/data/simulation.hdf5
diff --git a/notebooks/data/simulation_data.hdf5 b/notebooks/data/simulation_data.hdf5
diff --git a/notebooks/simulation_data.hdf5 b/notebooks/simulation_data.hdf5
diff --git a/simulation_data.hdf5 b/simulation_data.hdf5
diff --git a/tidy3d/components/data.py b/tidy3d/components/data.py
@@ -167,9 +167,9 @@ def load_from_group(cls, hdf5_grp):
             kwargs[data_name] = np.array(data_value)
 
         # handle data stored as np.array() of bytes instead of strings
-        # for str_kwarg in ("field", "direction"):
-        #     if kwargs.get(str_kwarg) is not None:
-        #         kwargs[str_kwarg] = decode_bytes_array(kwargs[str_kwarg])
+        for str_kwarg in ("direction",):
+            if kwargs.get(str_kwarg) is not None:
+                kwargs[str_kwarg] = decode_bytes_array(kwargs[str_kwarg])
 
         # handle data stored as np.array() of bytes instead of strings
         # for str_kwarg in ("x", "y", "z"):

diff --git a/tidy3d/components/mode.py b/tidy3d/components/mode.py
@@ -6,7 +6,6 @@
 
 from .base import Tidy3dBaseModel
 from .types import Symmetry
-from ..log import log
 
 
 class Mode(Tidy3dBaseModel):

diff --git a/tidy3d/web/webapi.py b/tidy3d/web/webapi.py
@@ -253,7 +253,10 @@ def download(task_id: TaskId, simulation: Simulation, path: str = "simulation_da
 
 
 def load_data(
-    task_id: TaskId, simulation: Simulation, path: str = "simulation_data.hdf5"
+    task_id: TaskId,
+    simulation: Simulation,
+    path: str = "simulation_data.hdf5",
+    replace_existing=True,
 ) -> SimulationData:
     """Download and Load simultion results into ``SimulationData`` object.
 
@@ -263,13 +266,15 @@ def load_data(
         Unique identifier of task on server.
     path : ``str``
         Download path to .hdf5 data file (including filename).
+    replace_existing: ``bool``
+        Downloads even if file exists (overwriting).
 
     Returns
     -------
     :class:`SimulationData`
         Object containing simulation data.
     """
-    if not os.path.exists(path):
+    if not os.path.exists(path) or replace_existing:
         download(task_id=task_id, simulation=simulation, path=path)
 
     log.info(f"loading SimulationData from {path}")

diff --git a/tidy3d_core/convert.py b/tidy3d_core/convert.py
@@ -9,7 +9,7 @@
 from tidy3d import VolumeSource, ModeSource, PlaneWave
 from tidy3d import GaussianPulse
 from tidy3d import FieldMonitor, FieldTimeMonitor, FluxMonitor, FluxTimeMonitor
-from tidy3d.components.monitor import AbstractFieldMonitor, AbstractFluxMonitor
+from tidy3d.components.monitor import AbstractFieldMonitor, AbstractFluxMonitor, ModeMonitor
 from tidy3d.components.monitor import FreqMonitor, TimeMonitor
 from .solver import SolverDataDict
 
@@ -241,18 +241,6 @@ def old_json_sources(sim: Simulation) -> List[Dict]:
         if src:
             src_list.append(src)
 
-        # """ TODO: Support PointDipole as a subclass of VolumeSource """
-        # elif isinstance(source, PointDipole):
-        #     src = {
-        #         "name": src_data.name,
-        #         "type": "PointDipole",
-        #         "source_time": src_time,
-        #         "center": source.center.tolist(),
-        #         "size": source.size.tolist(),
-        #         "component": source.component,
-        #         "amplitude": float(source.amplitude),
-        #         }
-        # """ TODO: Support PlaneWave """
         # """ TODO: Support GaussianBeam """
         # elif isinstance(source, GaussianBeam):
         #     src = {
@@ -303,65 +291,63 @@ def old_json_monitors(sim: Simulation) -> Dict:
         For that, and more generally, it seems that currently the Simulation doesn't have a
         TimeGrid or somethng like it? This is also needed e.g. to plot the source dependence, etc.
         """
-        if isinstance(monitor, FieldTimeMonitor):
-            store = []
-            if np.any([field[0] == "E" for field in monitor.fields]):
-                store.append("E")
-            if np.any([field[0] == "H" for field in monitor.fields]):
-                store.append("H")
-            mnt.update(
-                {
-                    "type": "TimeMonitor",
-                    "t_start": 0,
-                    "t_stop": sim.run_time,
-                    "t_step": None,
-                    "store": store,
-                }
-            )
-        elif isinstance(monitor, FluxTimeMonitor):
-            mnt.update(
-                {
-                    "type": "TimeMonitor",
-                    "t_start": 0,
-                    "t_stop": sim.run_time,
-                    "t_step": None,
-                    "store": ["flux"],
-                }
-            )
-        elif isinstance(monitor, FieldMonitor):
+        if isinstance(monitor, AbstractFieldMonitor):
             store = []
             if np.any([field[0] == "E" for field in monitor.fields]):
                 store.append("E")
             if np.any([field[0] == "H" for field in monitor.fields]):
                 store.append("H")
+            if isinstance(monitor, FieldMonitor):
+                mnt.update(
+                    {
+                        "type": "FrequencyMonitor",
+                        "frequency": [f * 1e-12 for f in monitor.freqs],
+                        "store": store,
+                        "interpolate": True,
+                    }
+                )
+            elif isinstance(monitor, FieldTimeMonitor):
+                mnt.update(
+                    {
+                        "type": "TimeMonitor",
+                        "t_start": 0,
+                        "t_stop": sim.run_time,
+                        "t_step": None,
+                        "store": store,
+                    }
+                )
+        elif isinstance(monitor, AbstractFluxMonitor):
+            if isinstance(monitor, FluxTimeMonitor):
+                mnt.update(
+                    {
+                        "type": "TimeMonitor",
+                        "t_start": 0,
+                        "t_stop": sim.run_time,
+                        "t_step": None,
+                        "store": ["flux"],
+                    }
+                )
+            elif isinstance(monitor, FluxMonitor):
+                mnt.update(
+                    {
+                        "type": "FrequencyMonitor",
+                        "frequency": [f * 1e-12 for f in monitor.freqs],
+                        "store": ["flux"],
+                        "interpolate": True,
+                    }
+                )
+        elif isinstance(monitor, ModeMonitor):
+            num_modes = max([m.mode_index for m in monitor.modes]) + 1
             mnt.update(
                 {
-                    "type": "FrequencyMonitor",
-                    "frequency": [f * 1e-12 for f in monitor.freqs],
-                    "store": store,
-                    "interpolate": True,
-                }
-            )
-        elif isinstance(monitor, FluxMonitor):
-            mnt.update(
-                {
-                    "type": "FrequencyMonitor",
+                    "type": "ModeMonitor",
                     "frequency": [f * 1e-12 for f in monitor.freqs],
-                    "store": ["flux"],
-                    "interpolate": True,
+                    "Nmodes": num_modes,
+                    "target_neff": None,
+                    "store": ["mode_amps"],
                 }
             )
-        """ TODO: support ModeMonitor """
-        # elif isinstance(monitor, ModeMonitor):
-        #     mnt.update(
-        #         {
-        #             "type": "ModeMonitor",
-        #             "frequency": [f * 1e-12 for f in monitor.freqs],
-        #             "Nmodes": mnt_data.Nmodes,
-        #             "target_neff": mnt_data.target_neff,
-        #         }
-        #     )
-        #
+
         """ TODO: Support PermittivityMonitor """
         #
 
@@ -439,8 +425,20 @@ def load_old_monitor_data(simulation: Simulation, data_file: str) -> SolverDataD
                         "values": field_vals,
                         sampler_label: sampler_values,
                     }
+
             elif isinstance(monitor, AbstractFluxMonitor):
                 values = np.array(f_handle[name]["flux"]).ravel()
                 data_dict[name] = {"values": values, sampler_label: sampler_values}
 
+            elif isinstance(monitor, ModeMonitor):
+                values = np.array(f_handle[name]["mode_amps"])
+                values = np.swapaxes(values, 1, 2)  # put frequency at last axis
+                mode_index = np.arange(values.shape[1])
+                data_dict[name] = {
+                    "values": values,
+                    "direction": ["+", "-"],
+                    "mode_index": mode_index,
+                    sampler_label: sampler_values,
+                }
+
     return data_dict